I had a problem develop after I removed and replaced the intake manifold. The one difference this time was that I took the rubber boot that connects the afm to the plennum off, instead of just pulling it off the afm and leaving it on the plennum. When I put it back, it looked like it wasn't quite bent the same way as it was when I put it on. Upon starting, the car sat at 200 rpm with the lights blinking, before slowly working its way up to 1k. The car would almost die when putting the clutch in, barely staying alive and working its way up to idle, as well as having an idle around 750.

This was all when the car was cold, once it warmed up, it seemed fine. When I went back and looked at the boot, I could see a few hidden, but large, cracks. They had been there for awhile, I guess I just tweaked them when I put it on a bit differently so the intake leak was more pronounced.

I thought I'd post this as maybe a first thing to try/look for with a cold idle problem, since it's only $20.

I had a slight thumping noise from the exhaust at idle, I haven't checked to see if it's gone, and I think the trailer hitching of off to on throttle is less pronounced as well.