I did my LS swap 17 years ago, and fought the factory wiring in my CJ5 for about 5 years before I finally replaced it all with a kit from Centech. I'm sure the Painless kit would be a good one as well.
If you are doing an LS swap with a manual transmission, buy the Centerforce clutch with the weights on it. The weights will help apply pressure to the clutch disc to prevent slipping at higher RPMs, but still gives a soft easy pedal feel in traffic.
I did all custom gauges and dash in my CJ, while it is really cool, looking back I do regret it and wish I fixed my factory gauges. Those would be cooler. Do the tough wiring and try to make your factory gauges work.
I hate to say it but the "buy once cry once" crowd really do know what they are talking about. I've had my project for long enough now that I've learned every lesson they tried to help me with the hard way instead of listening to them.
I'm sure I have more, I'll try to come back and edit this as I think of more.
