find your starter relay. Locate Pin 1 (has a black wire going to it on plug). And then apply 12v to it. do this with the key in the On position. The car should start when you do this or at least crank if you have everything hooked up right. This is the fool-proof absolute bypass of everything else before the starter solenoid itself.
Also, i want to ask...are you re-using the old A/T ECU or did you swap it out for a M/T ECU?
**Edit: Note that ive read that the starter relay is located in the No. 2 Junction block in the engine bay.
Location of Starter relay.