Do you have an SES light? Might be a good time to scan for codes. (Edit -- duh, motor swap. Do you still have the ALDL port in the wiring harness?)
Does the motor turn over when you turn the key? Or is it just completely dead?
Does this only happen with the motor warmed up? I would tend to lean towards an ignition problem. Sometimes the ignition control module / coil start to screw up once they get hot. But, it could just as well be a wiring problem -- did you check for any burnt wires (around exhaust and whatnot)?
I'll let someone else step in...