Idle issues and backfiring

I've been experiencing issues with my 97 2wd auto xj for the last several months. Current mods are a 95 head, a 99and up intake, cold air, header, and 2.5 exhaust all the way to the header. It starts up no problem, I never have to crank it, but once it starts warming up, it begins idling rough. If I'm driving it, it will bog down, then backfire several times, then smooth out when it gets to operating temp. If its just idling, then it will go through a couple cycles of idling very rough, then smooth itself out. More recently, it continues to stay rough at idle till I put it into gear, but putting it back into park or neutral results in poor idle again. I recently noticed a knock and originally thought it was a rod knock, but I read elsewhere that this could be the flywheel. My transmission hasn't been shifting properly and so I'm beginning to suspect that might be at least part of the problem. Once it gets going, it runs like a champ, so i'm really frustrated. Any help or suggestions? Anyone experience something similar?

You ever figure out this issue?

The exhaust manifold was warped and cracked in 3 places