Well I figured I'd update my thread with what I found to be the real cause. I know that it was mentioned before, and they were right, it was a vacuum leak at the number 1 and 2 cylinder where the manifold mates to the head.. and this vacuum leak was caused by an interference in fitment with my APN header.. I discovered this after pulling the intake manifold and noticing that the gasket around those 2 intake ports was darker than the rest, and there also was no impression created by the intake manifold. Upon further inspection, I saw a small crease in the top of the exhaust manifold number 1 tube.. the bottom of the intake manifold was making contact with the top of the exhaust manifold, i guess I torqued it down pretty good too, because of the dent that I created in the tube. If I would have removed it for inspection earlier, before I started throwing parts at it, then I would have been able to just grind down a small part of the intake to clear the exhaust..

Well I had already ordered a 2001 intake manifold because I thought that my original was cracked. I did end up with even more clearance issues, but this time it was the number 6 exhaust tube that was hitting the bottom of the newer intake.. no problem, a little grinding of the intake and a little MAPP gas and a hammer to the exhaust and I was good to go.

Final results of the intake did not give me the gains that I was ecpecting, it didn't feel like it added any power at all, but at least I am running smooth again, no more rough idle, no more struggling in overdrive..

I think I have learned a TON about the XJ, I have only owned it for 4 weeks and have already installed a RC 3" series 2, chased down this intake leak, swapped to a newer manifold, oil pan gasket (royal PIA!), and rear main seal.

I have definatley popped my XJ cherry