Nice! My guess is that the transmission swap was done with an older LSD tranny which didn't have a crank position sensor location. If you look at the part of the bellhousing that faces toward the front of the car there should be a small sensor held one with a 10mm bolt. If this is not there, that is your problem. If there is a sensor there it is possible that the wrong ecu is in the car or that the flywheel used does not have the proper tooth count for an OBDII application (nissan had these on OBDII in 95 even though it wasn't necessary until 96).