The original wiring harness was in dangerous condition. There were large sections of cracked or missing braided insulation, exposing bare wire. To make things worse, in the original configuration, there were no fuses and only one circuit breaker in the entire system. The circuit breaker only protected the lighting and brake light circuits. The circuit breaker is mounted on the back of the light switch. Some versions used a jumper wire from the circuit breaker to feed the light switch. Other versions had this feed incorporated into the circuit breaker mount.
(My earlier comments on the circuit breaker connections were wrong. Despite this startling revelation, I cannot be held responsible for earthquakes or other unexplainable phenomena which may result.)
Understand I like fuses and circuit breakers. I have seen first hand the serious problems caused by damaged insulation. I'm pretty partial to keeping things original when possible, but this is one upgrade I consider essential. Unless you're building a 100% stock show vehicle, your electrical system should include fuses or circuit breakers. The possibility for severe damage is just too great.
Replacement harnesses are available from several Willys vendors. You can get plastic or braided covered wire. The braided wire available today is a braided sleeve over modern plastic insulation, combining the best of both worlds. It looks so nice under the hood. With my new harness several years old, I have noticed the braided insulation really holds dirt and grime. Unless you are trying to replicate the exact original appearance for a show vehicle, you might find modern plastic wiring more suitable.
A reproduction braided harness is not cheap. A new harness can be ordered with various upgrades like turn signals, etc. if desired. Building a new harness is not hard at all so that is the route I took.
I ordered my supplies from Rhode Island Wiring Service. There are other suppliers, but I highly recommend these guys. One nice touch is that you can order the various color and gauge wire by the foot, unlike other vendors. If you know exactly how much you need, you can save a lot of money that way. To keep my total cost down, I only used braided wire where visible under the hood. I used marine grade plastic coated wire in the non-visible areas, like under the dash and for the tail lights. Stay away from the cheap wire sold in rolls at places like Pep Boys. (As a general rule, stay away from Pep Boys, regardless.)

Here is a picture of the fuse block I added under the cowl, on the aft side of the firewall. My original thinking was to keep it well out of sight to help keep the original appearance. Now I wish I had put it in a more accessible spot. If you choose to locate the fuseblock under the hood, make sure it is well protected from rainwater running down the firewall. The flasher and front turn signal relays are next to the fuse block. The shadows in the picture make the wiring look tangled above the fuse block:

The original ignition switch was in the base of the coil. The coil was mounted under the dash pointing forward so the switch came through a hole in the dash. This arrangement was only produced for a few years and then a separate switch and coil were used. The integral coil/switch was no longer available as a replacement after the original stock was depleted. The original coil/switch was long gone when I bought the Jeep. I thought long and hard about where to mount the switch. With the original configuration, it was a pain to reach across to the switch while working the choke. A mystery hole on the left side of the dash came to good use when I moved the switch there:

Unless you rolled your Jeep straight out a time capsule, it is common to find a true rat's nest of wiring. A wire was added here and there for new accessories. Often damaged wire is bypassed and the original pieces left in place even though they are not connected. I found all of this and more on my Jeep. There was even Romex household wiring running back to the tail lights. If your wiring is not too bad, you may want to string any replacement wires in place one at a time. My wiring was completely shot, and on top of that I hate crawling on my back any more than absolutely necessary. It was time for the harness to come out.
For safety, disconnect the battery first. Now don't just start attacking with a pair of cutters. Consider how the harness was likely installed at the factory. Carefully mark any connections that will be undone. Mark any critical dimensions such as exactly where the harness passes through the firewall, etc. Make note of any wires that are too tight, perhaps from previous repairs, and should be a bit longer. Under the dash, only the fuel gauge and ammeter need the wires disconnected. Remove the headlight and ignition switches, etc. from the dash with their wiring still connected. That saves a lot of time and effort to unhook all those wires in close quarters. Under the hood, free the harness from the grill junction block, horn, brake and dimmer switches, etc. There should be a pair of quick disconnects to separate the harness running aft to the tail lights. Pull the main harness aft through the firewall. The only messy part is extracting the harness for the tail lights. I had the front clip off already, making it easier to access the wiring on the backside of the grill.
On a sheet of plywood, spread out the remains of the old harness. Straighten it out as best you can. With some small finish nails, secure the harness in this spread out position. Whenever practical, keep components like the various switches with the harness. Put a single nail in any unattached ring terminal and label it. Drive in a pair of nails on either side of the harness every few inches. This pathway of nails will form a guide to build up a new harness right on top of the old.
For certain items like the tail lights, I'd suggest leaving that section long and install the terminals after the new harness is reinstalled. Otherwise, use the same lengths unless you noted a problem before. Resist the temptation to add "Just a Little Bit" to every wire. I did that in a couple of spots and ended up with loops of wire in the way after installation. The nails in the wire terminals indicate the exact length needed if the old harness fit. This was especially critical where several wires terminated at one spot, like at the junction block for the grill.
I decided not to duplicate the quick disconnects for the tail light harness. That was used in the factory when the prewired tub was installed on to the prewired chassis. Should I ever pull the tub, I'll cut the wires and add quick disconnects. But for now, I have a more reliable harness with fewer joints.
This picture shows some of the supplies you will need to build a long lasting harness. Invest in a good pair of crimpers. The quality of the harness depends on it. Beg, borrow or steal an automatic wire stripper. It will save an incredible amount of time and give consistent results with no damage to the wire strands. I purchased the terminals locally at an electrical supply house. Make sure you get brazed barrel terminals. All that means is the barrel portion is brazed to form one continuous loop. Cheaper terminals don't have this feature and the barrel seam will separate when crimped. Brazed barrels make a big difference in longevity of the connection. I used uninsulated terminals, and finished them after crimping with a short piece of heat shrink tubing. This looks nearly identical to the neoprene rubber sleeve originally used. You could use insulated terminals but they will look funny with braided wire. Last but not least is some dielectric compound. Coat every wire end and the inside of each terminal barrel before crimping. This will not affect the conductivity but will prevent any corrosion from forming:

You may wonder how could you solder the terminals if that dielectric compound is in the way. I strongly discourage soldering the terminals. Soldering will give an excellent conductive path but is more prone to damage from vibration. The solder will wick up inside the wire strands and form a rigid point against which vibration will be concentrated. It is very common to find soldered joints with broken strands right at the end of the solder. A properly crimped terminal does not concentrate the stress of vibration. Many of the reproduction harnesses feature soldered connections which helped me decide to make my own. Should you decide to solder your terminals, use a quality non-corrosive flux. Use as little solder as possible and work from the end of the wire strands. This will minimize solder wicking up beyond the terminal barrel.
Several words of caution about the dielectric compound are in order. It looks just like uncured silicone adhesive. Don't use silicone, thinking it will work better and you just so happen to have an extra tube in the shop. Silicone rubber contains acetic acid and will corrode your connections from the inside out. Also, don't use conductive compound even though that seems to make more sense inside a terminal. The problem is if some conductive compound were to ooze out into the wrong area. It could cause a short circuit. Dielectric compound is electrically neutral and will not prevent current flow inside a terminal nor will it cause a problem if it leaks out.
If you have followed along this far, you may be pretty serious about building your own harness. Before you continue, raise your right hand and swear that you will not wrap the harness with vinyl electrical tape. Go on, raise your right hand and say it. I'll wait.
The original harness was wrapped in a special type of rubber tape that has no adhesive. This stuff is truly amazing, and the only thing it will stick to is itself. But be careful, because it looks very similar to black vinyl electrical tape. You could do a fantastic looking job wrapping the harness with electrical tape and in a few months it will look horrible. The adhesive softens and gets gummy while the plastic gets brittle. Wire will be exposed as the tape slips or cracks. Dirt and grit will stick to the adhesive.
I don't know the exact composition of the original harness wrapping tape, but a modern replacement called Cold Shrink Plastic Wrap is readily available. Order the 1" Black Tape (Newark Electronics part #95F1132) to match the original. Two rolls should be plenty. This tape is used extensively in aviation wiring and I will vouch it is incredible stuff. I redid my Jeep's wiring harness several years ago and it shows no sign of deterioration. It is hard to fathom how it goes on easily, and can be repositioned as needed for the first few hours. After it has set overnight, it fuses to itself and would have to be cut off. Part of the secret is to stretch it slightly during application.
Edelbrock #9359 PowerBond self-sealing wrap (NAPA #BK735-2538) appears to be the same stuff and is readily available from nearly any parts store, but only comes in a small 16' roll. Sports fans may be familiar with a similar product called Hockey Tape, but I don't know how that would stand up under the hood.

Here is a shot showing part of the installed harness. This is the junction block on the driver's side fender. Note how the main harness is wrapped. You can see how the wires to the horn come out in between wraps. The wrapping started at the front and worked towards the firewall, making it easier for individual wires to exit the harness. The harness for the grill wiring has a braided sleeve instead of the wrapped construction. This sleeve is available from vendors of braided wiring. To make the lighting circuits more reliable, I've added a ground circuit. The headlights were originally grounded through the buckets and then the grill, to the frame and finally back to the battery. That is a pretty arduous path requiring bare metal-to-metal contact at every junction. I extended the ground wires to meet at a larger junction block, where several of the terminals are ganged together as a common ground. A single ground wire runs under the radiator and joins the ground cable from the battery's negative terminal.

When reinstalling the harness, pay attention to the wire routing near the headlight dimmer switch. I didn't consider the travel of the clutch pedal and it caused a chafed spot in the insulation.
Details about eliminating trouble spots in the fuel gauge circuit can be found in Fuel Gauge 101.
A 6 volt starter will draw a lot of current, approximately 225 amps, with an initial surge around 350 amps. That is a huge amount of current which will tax marginal cables. The original cables were long gone on my Jeep. Since I wanted the best performance from the 6 volt starter, I deviated from the stock cable size and routing. I have no idea what gauge was originally used. A quick check of an electrical textbook showed I'd need massive 4/0 cables to handle 350 amps. I could have gotten away with 2/0 cables and ignored the initial spike but I wanted to be on the safe side. If not sure if your existing cables are up to snuff, check their current-carrying capability with a very simple voltage drop test.
Premade cables from a parts store are generally not even remotely capable of handling that current, resulting in very slow cranking speed. This type of cable often has a thick layer of insulation to disguise the relatively thin wire inside. The conductor inside 4/0 cable is about as thick as your thumb. A good auto electric shop can make up the proper capacity cables, or you can make them yourself. This shot shows a battery cable crimper installing the terminal lug for the starter motor:
That battery cable crimper is not something you will find in the average shop. I found this one used and somehow snuck it past the finance committee. A new one runs several hundred dollars. Ancor Marine manufactures an excellent low-cost bench mounted alternative. It is available online from WestMarine.com, part # 214080.
In this image, the battery post terminal is being crimped in place. I don't really care to discuss how I know this, but the positive battery post requires a larger diameter terminal than the negative. Make sure you purchase both sizes for building the cables:
Such large terminals are not always easy to find. NAPA carries them, although they don't show up at their website. For the positive terminal for 4/0 cable, ask for NAPA #728054. The negative terminal for 4/0 cable is NAPA #728055.
After the cables are crimped in place, slip a short sleeve of heat shrink tubing over the joint. If it won't slip over the terminal, you will have to remember to slide the sleeve to the middle of the cable before adding the terminal. No, I don't care to talk about that either. Red heat shrink tubing is available if desired to mark the positive cable ends.
I chose marine grade cable for the extra durability, available at NAPA along with the terminals. Welding cable might work well but I don't know about the insulation's durability under the hood, so choose carefully. Please promise that you won't buy those bolt-on "Emergency" battery terminals. These are the type often seen on the parts counter next to the pine tree air fresheners. If I were ever stranded by the side of the road with an electrical problem and had one of those emergency battery terminals with me, I could throw it to flag down a passing car. Other than that, they are pretty much useless.
Running a 4/0 battery cable to the starter terminal only covers half of the circuit. The ground leg of the starter circuit is equally important. The original ground path was quite torturous. From the negative battery terminal, a short lead ran to the frame in front of the battery. At the right front motor mount, a strap ran from the frame to the engine's front plate, shown in the front view below. The front plate sits on a gasket, so all that current had to flow through the mounting bolts to reach the engine block and the starter. The ground strap across the motor mount often gets lost during an engine change, leaving the current to find the path of least resistance. That could be your throttle cable or clutch linkage. A friend had his throttle linkage start smoking with the starter engaged since the ground strap was missing. Even with all components in place, the stock ground path is marginal at best:

The ground path was beefed up by running a 4/0 ground cable directly between the battery's negative terminal and a starter mount bolt. That eliminates any potential problems in the original ground path. A smaller cable, which doesn't need to handle the massive starter current, runs from the battery terminal bolt to the frame. Another small cable grounds the voltage regulator, which previously relied on the fender sheet metal. While not shown in this picture, the generator's ground is included in the short harness which runs to the voltage regulator: