Mine is a 2001, I didn't get the computer from the 99 the motor came out of, everything bolted in though, the only differences were the cam sensor and coil packs

 

So I cleaned my IAC, no change, but my dad started messing with the cam sensor and it seemed to change the timing. Does anybody know if bad timing can make the motor go haywire like that?

 

Well my 99 xj does not have coil packs
So I am just throughing out random thoughts
Coil packs take over the place of the distributer
You may want to check them out with a ohm meter
Maybe 4.0 liters are set up different that have distributors vs coil packs
Food for thought good luck