Idle Problems in CRX after trans swap

[GasSavers_Hal9000]

I've been fighting this problem on and off for about a month now (mainly because I don't drive the car much during the winter). So far the guys at honda-tech and hondaswap haven't been able to help... I'm hoping somebody here has a few ideas:

The car: 88 Honda CRX DX. Originally AT car, recently swapped to stock DX trans (ECU also swapped).

The problem: After the swap, the car seems like it never comes off the warmup cycle. Idle is always high (1100-1700 depending on who knows what), but will drop to 750 if I blip the throttle like you would with a carbureted car to knock it off the fast idle. The next time I rev the engine it goes back to the high idle. It also pulses between 1100-1400 on rare occasions (only twice in the past month). The RPM also seems to drop more slowly than it should (or not at all) between shifts as if the ECU is keeping it artificially high.

What I've checked:
1) engine codes - none
2) coolant system - properly bled and filled
3) ICV - cleaned
4) linkage - inspected and lubricated. No binding or other problems. Vacuum actuators, appear to be working properly, but it's hard to tell for certain.
5) Sensors - need to test, but can't find anything to compare the values to.

I'm down to thinking that it's either a bad temp sensor, or maybe a bad O2 sensor that's spoofing the ECU. Aside from that I have no ideas except maybe that there was a wiring difference between the auto and manual ECU that needs to be changed. All I swapped was the Neutral cutoff and backup light wires. Everything else was just plug and play (or maybe I'm wrong on that?).

Any help or troubleshooting advice? Now that the weather is warming up again, I'd like to get this resolved so I can drive the car on a regular basis.