Ok, let me start from the beginning. I've read through a ton of posts on here and FB and Reddit about this issue. I understand it could be a million different things, and I've thrown tons of parts at it which I know isn't always the answer, but I was frustrated.
A few months ago, I swapped the intake manifold for one off a D16Y8 auto from a 99/00 Civic and used my throttle body from my original D16Y7, so the IACV (three wire) is on the bottom of the throttle body. Other than the intake manifold swap, the car is completely stock.

Here's what I'm experiencing...after completing the intake swap, I double checked everything and completed the stuff listed below. As well as doing a idle adjustment (Photobucket | picture_4760.jpg). But I cannot get the idle below 900-1000 rpm, even if I tighten down the idle adjustment screw all the way closed (which I don't expect is correct). I'm monitoring RPM on my external tach. I've been driving it around but I started to notice after driving for several miles, the car starts idling higher at stops, around 1200 RPM and when I give it a little gas, it surges as it passes RPM between 1200-1500 during acceleration but will push past that and then it's accelerates normal-ish, minus when this happens there is very a noticeable jerking when coming on and off the accelerator pedal.

When I get back home, I connect up my OBD scanner and I get a P05050 code, IACV...but I honestly don't think that's it. More like that's happening because of the high idle condition and the IACV is acting up due to the base idle not being correct from the get-go.

Only thing I noticed after so more testing was that when I pinch closed the vacuum line that runs from the PCV valve to the intake manifold, the idle drops. Is that significant to my condition? I have no idea. And getting that PCV is a PITA because I have to take off the intake manifold to get to it. The one I replaced it with about 1 month from OEM from Honda. Just not sure if that behavior of me pinching the pipe and the idle changing denotes anything significant like the PCV is bad or something.

Things I've replaced/checked:
Breather box - Removed, cleaned, and new o-ring installed
PCV Valve - Replaced
TPS - Replaced and calibrated, ~.50 closed, ~4.30 WOT
Throttle cable - adjusted, about a 1/4 inch slack
ECT - Replaced
Fan switch sensor - Replaced
MAP - Replaced
Throttle body - heavily cleaned
IACV - Replaced, twice (Aftermarket)
Vacuum leaks - smoke tested, zero leaks
Flushed and filled coolant system - burped multiple times, raise front end with jack and burped again