I redid the wiring harness in my 80 CJ5, it was a bitch, but with a good FSM, it shouldn't be too bad. Look on ebay and see if you can find a real factory service manual for your year. It will make everything much easier. I don't suggest you get a Haynes or Chilton manual, from what I've seen the wiring diagrams are useless and the vacuum diagrams probably are too. As for the vacuum lines, you can probably get rid of most of them, they are for a bunch of emissions bullshit that probably doesn't function any more. You should really only need a vacuum line to the distributor, to the PCV valve, and to the brake booster if it has power brakes. The rest can probably be capped.
Jeeps don't break things, their schedule for upgrading weak parts just gets a new time scale on occasion.