Tom,
Related to the 5MT tranny and OBDII question, I've gotten lazy and haven't solved the check eng light. Thanks for asking. The code has to do with the TCU no longer being present. I was freaked out about smog check, but it went fine. Lucky for me the CE light doesn't come back on for a couple days until after reset
The local smog test guys also didn't seem to care that it had a 5MT vs an auto. Oddly their computer had manual as a selectable option. Looks like you've pimped your ride pretty nicely. Now if I can just get the rattles out of the doors when the stereo is turned up I'll be really happy.