anti-theft?????PLEASE HELP

First of all I have a 99 chevy cavalier 2.4 I just finished installing a new clutch in my car and had the battery out for a while now the car will not stay running. I have had problem before even doing the clutch with it starting then stalling almost immediately but I always eventually got it started. I have looked and looked and I keep reading on the anti theft or passlock problems. I have tried the 10min intervals over thirty minutes also waiting an hour and still nothing. I am at a loss I don't know what to do I have already but enough money into this dam car already. I tried reading the codes and at first it did tell me that the throttle positioning sensor, so I replaced it now its not reading any codes and I still cant get it to stay running. any ideas on how to bypass or even get it started.
PLEASE HELP

I replaced my engine/trans. When I was done, it would actually start but shut down immediately due to the anti theft. Have a full charged battery. I was told it does not like the voltage drop. I was told to keep a 10 A charger on it for the run. I didn't do that but I did charge the battery before I did the procedure. And was given these figures 12.65V - Full Charge. 12.45 half charge, 12.25V quarter charge. I had the 12.4Volts and did fine.
Do the turn to start then to the ON position. It will try to start but doesn't. Theft light is on (mine was blinking) and watch it. After about ten minutes it will turn off (or stop blinking like mine did). Wait for it to turn off or stop blinking like mine. It is not a time but a function complete procedure. When it stops blinking/ or turns off, repeat same procedure. Then do it a third time. Should start after that. The computer is talking to all the sensors, and other modules during this time. Wait for it to turn off or stop blinking like mine was. Should work. I have a 1999 but with the 2.2L. Post your results.Goodluck
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Hope this posts only once. When I looked at the posting, it was missing. So I added again. If it repeats, sorry.