i put an s14 transmission into my s13. as of now, there is no wiring hooked up to the transmission whatsoever, and its probably going to stay that way with exception being the speedo sensor, which i need to get an s13 sensor, since the plugs to the harness do not match up. also, i just took of the angle sensor from the transmission before i put it in.
wiring isnt really clarified too much either. all i have done is wire it up to start, so i'll explain in detail how to do it for those interested. theres a 2 prong plug that is on the engine side of the harness, below the three that are fixed onto the side of the fuse box, find the plug on the auto transmission harness and cut the wires about 3" away from the plug, then striip the ends of the wires from that plug and connect them. you can put a cap on it or whatever to protect it if you want. then all you do is plug it into the matching plug on the engine harness and everythings good to go as far as starting is concerned.
what your doing there is fooling the ecu into thinking the car is always in neutral, but this will not affect the way the car drives, just make sure not to start the car in gear or with the clutch not depressed.
also, the s13 driveshaft is completely different from the s14 driveshaft. i ran into this problem when i bought the s14 transmission and driveshaft in a combo.
another problem i have found is the dust cover on the tailshaft of the s14 trans will hit the s13 driveshaft and it will not fit. the only way to get it to fit is to take the cover off and you can try to get an s13 one to put on, but i have just left it off.
the rear portion of the automatic driveshaft will also work with the front portion of a manual driveshaft. so there is no reason to remove the driveshaft from the differential.
just thought i'd share this info because these things are what caused me the most trouble doing my swap. other than these few things the guide on 240sx.org along with an fsm will guide you through everything pretty easily.
