There is another possible reason the car wouldn't start with the manual ECU. If the car the manual transmission ECU came from had an immobilizer, then you will need the key from that car to start it. Were you still using your key? Do you even have the key from the manual transmission ECU car? If your car doesn't have an immobilizer and the manual tranny car did, it will never start, because I presume you don't have the key reader in you steering column. If both cars had immobilizers, and you don't have the key to the manual tranny car, you will have to have your key reprogrammed to match that ECU, but I think you need the VIN of the manual tranny car to do that. I'm not sure. I think there is a way to do it yourself in the car, but I don't recall how.
It's also not weird that the car started when you pushed in the clutch with the auto ECU installed. You said in your first post that the clutch was depressing the start switch. In this diagram, which you should have gotten before doing this swap, you can see that all the neutral start switch does (blue arrow) is connect the two points marked with the green arrows. Well, you installed the clutch switch (red arrow) which now performs that purpose, but only when the clutch is pressed.
Another thing to consider, if you keep the auto ECU is that the computer is going to try to shift the transmission by sending out signals to the shift solenoids. From the book, I quote, "When shifting to 1st speed, current flows from TERMINAL S1 of the engine control module to TERMINAL 3 of the electronically controlled transmission solenoid to GROUND, and continuity to the No. 1 solenoid causes the shift." In this diagram, the one you should have, that would be flow from the red arrow, to the green arrow to the blue arrow. If the shift solenoid is not present this connection will be open circuit. On later model cars, the ones with the 3mzfe engine, the ECU will retard the timing when the car is shifted. If you don't connect the shift solenoids (or something that acts like them) the ECU will not act as it should and the car may accelerate like crap. I'm not really sure how it will act, because I don't know if these early model cars altered the timing or not, plus I don't drive automatics and so I don't know much about them. But I would assume so because it is, after all, an electronically controlled transmission. trd4life (this website) has confirmed that the engine will run poorly on an auto ECU if you don't simulate the solenoids. And warning, I wouldn't just connect them straight to ground. Measure the resistance of the solenoids and connect them to ground through similar resistors. Otherwise, it may sink too much current and burn out that part of the ECU. Just a thought.
Good luck with your swap. I hope it works out for you.
by TxBmbleBee » Wed Aug 19, 2009 7:48 pm 
