ODB conversion help.

OK so I did a motor swap in my 97 EK hatch (ODB2A). I put in a 94 LS motor (ODB1). I hooked up the hatch's wiring harness to the engine, and I am still using the ODB2 ecu. I can start it, but when it is cold it has a real rough idle (bouncing idle between 1500 and 2000 rpm). Once it warms up the idle flat lines and balances out at about 1000 rpm.

After it warms up and i step on the gas to slowly and steadily increase the rpms it doesn't increase smoothly. between 1500 and 2000 rpms it still bounces, once it past 2000 rpm its fine. I do have a CEL on it says O2 sensor (secondary) and Idle Air Control Valve, but I have cleaned and replaced the idle air control valve part more than once and that didn't fix it.

Any ideas? Should I switch to the ODB1 ecu? (if i do this will I still be able to pass emissions?)

You need the OBD1 ecu and no, you wont be able to pass emissions

I'm guessing that your car originally came with a non-vtec D-series engine. The non-vtec Civics (and automatic ones) from '96-'00 had a 3-wire IACV, where the '92-'95 Civics & Integras has a 2-wire IACV. That would explain why you are throwing that code. Here's some info on what to do, if this is indeed the case:
http://www.ff-squad.com/tech/wiring/wiring.96-98.jpg
http://www.ff-squad.com/tech/wiring/wiring.96-98_a-plug.jpg

CivicSpoon (http://www.automotiveforums.com/vbulletin/member.php?u=38745) with your advice is it possible to still run the motor with the ODB2 ecu?

It will run, but you should get a '96-'98 P75 (Acura LS/RS/GS) ECU. Otherwise, you're going to be running on the fuel and ignition timing maps for a SOHC D-series engine (whatever your stock engine was). By doing that you're going to be running lean, and performance will definitely suffer.

I've already had all the wiring done but just running on the wrong ECU hopefully that should solve my problem... but now where to find a cheap ECU... or cheap chipped ECU online?