Well, Normally I say the Idle Air Passage is the culprit for a rough idle, but actually it's only one of the problem areas. Seems the TPS can cause one helluva rough idle. Just replaced the one in my ZJ because of some rough idle and surging (downshift) on highway when letting off the gas.
The idle is now smoother than it's been in years. But the shifts are a bit smoother as well, I prefer more of a "HERE'S YOUR DANG GEAR!" shift. That's something I can adjust though.
Makes sense when I stop and think about it, which is probably why my head hurts. :)