The manual trans clutch swith is under the dash, up on top of the clutch pedal assembly, just follow it up from the pedal to the top of the shaft-thingy. I didn't think of this earlier, probably should have, though. Check for loose wires, etc.
The one on the trans you are thinking of, it doesn't have anything to do with the starting circuit, it's a sensor for the ECU to tell it when the tranny is in neutral, so the ECU can predict ahead of time when it should idle (such as coming on a red light), there is also another sensor on the clutch for this same reason-it has 4 pins, the one for the starter only has 2. I hope this helps at least a little.
If this doesn't help, I can tell you where ever connector for the starting circuit is, and you can check them all