I did a complete rewire years ago. Prior to that job, my experience with automotive wiring was installing a couple radios.
I bought a Painless harness. I stripped every existing wire out of the Jeep, and replaced the tub with a 'glass tub, then got started...
It took awhile, I was careful. And I had to ground everything independently because of the glass tub, so I had to terminate all my own wires (vs buying a pre-terminated kit)
When I was finished and ran the final test, everything worked!
It was not as difficult as I initially feared.
This was over 15 yrs ago...
If I was going to do another rig today, I'd use the 12-circuit harness from EZ Wiring.
You can often find these on ebay for even less than buying direct.
These are very good quality harnesses, priced far
less than Painless. Many of the guys on EarlyCJ5.net have used this harness any find it to be good quality, easy to install, and at a very good price.
Like Dempsey said above, I'd recommend going with a harness kit, and EZ is the one I would use.