Tercel Running Rough, Runs rough in gear Options

[Terseo]

I own a '92 Tercel DX but it's now a Terseo. (IMG:style_emoticons/default/banana.gif) After my engine blew I decided to swap it with a JDM 5E-FE and a 4-SPD Paseo Tranny. To make the transition easier I swapped out the ECU, engine and interior wiring harness with a '92 Paseo from the wrecking yard.

Last week I started the car for the first time and after timing it and repairing a few exhaust leaks it ran fine. (IMG:style_emoticons/default/57.gif)

Today I drove it down the driveway and it didn't go as planned. When I put it in gear it dropped about 500 RPM. The motor ran rough and the car was shaking a lot. (IMG:style_emoticons/default/frozen.gif)

It does this in every gear except park and nuetral. If anyone has any ideas I would appreciate your help.

Tomorrow I'm going to double check the engine mounts and also look at the mixture. Maybe its too rich. (IMG:style_emoticons/default/right.gif)

Thanks (IMG:style_emoticons/default/57.gif)