when you replaced the wiring, did you replace the ecu too? never know, could have been something stupid like the wires melted, caused a short, which fucked the ecu...

could also be the TPS.
In safe mode, it only reads the TPS. If it is off, and you add in a MAF signal, it could be tweaking out the ECU... kinda like dividing by zero.

the tranny sounds like the clutch itself. It might have been driving for a little bit, then broke.... clutch plate not aligned right will do that... pressure plate just dying will do that... throw out going bad, grinding away at the pressure plate splines until the ends snap off and get jammed between the clutch and the flywheel, gauging and scoring and melting and welding all kinds of mayhem in there will do that too...

EDIT:
oh, and if it is an 5 speed swap, if the kid forgot to change the pilot bushing, then the bearings could be shot.

could also be something dumb, like doesn't have any gear lube in it... or the gear selector shaft is warped/bent.