Welcome to the board.
Here is the RENIX manual with explanations and diagnostics.
http://pirate4x4.com/tech/billavista/PDFs/Jeep_Renix_Fuel_Injection_manual.pdf
And a wiring diagram, it's for an '88 but is probably 90% identical.
http://www.comancheclub.com/forums/viewtopic.php?f=9&t=12734
Almost as exciting as the 2006 NHRA Top Feul finals when another "Tony S." had to win the finals and set a national record to win the championship. I was on the edge of my seat for both.
I've seen caps that look similar to the originals (black with orange lettering) at O'Reilly Auto Parts. I'll get one tomorrow and let you know if it fits. Looks lik this.
http://m.summitracing.com/parts/RNB-82594
They seemed to be on there pretty good, I couldn't just pull them off with my fingers. My stock ones did not have them either.
I attached the thread (with pics) I was talking about, and precision responded eventually.
The ones you receive from precision will probably have blue tips and look more like a beanie, that's a stock photo. I asked this same question to precision (and on this board) and was told to leave them on. The rebuilt injectors come with new o-rings.
http://comancheclub.com/forums/viewtopic.php?f=2&t=31399
From what I've read, '95 & '96 don't require any modification other than new lines to the block. Make sure you get the aluminum spacer, it's between the foam seal and the booster. I have a '95 one awaiting install.
The XJ fan should fit.
Probably dealer only (if they still carry them) or at the junk yard for the tee. I've done this to mine and prefer the 2.5L overflow to a universal. It fits along the fender but the fuel pump resistor and the EGR solenoid(?) need relocation. I've always picked up the overflow at the JY, no help on getting one new. Seen used ones on eBay but usually pricey compared to JY.