L32 or not, would not effect how it ran. It's the same motor with a different blower. That wasn't until 04 anyhow..

Try resetting the PCM? Not really sure what the issue might be based on your description but I know after my swap my car would start up fro about 2 seconds then shut off. Turned out to be the PCM, which just needed to be reset, then I was in the clear.

*edit*
You said you checked spark, how about the coils? they the ones from the stock motor or the swapped motor?