Starting and idling problems

I was thinking it sounded an awful lot like the anti-theft stuff as well. That will let the car start and run for a few seconds, but will shut it down shortly after. I would think the flashed computer would have taken care of that, but you might check with Hotwire and see if there is any troubleshooting they could help you with to confirm that. I'd double check all sensor connections as well. Could be starting up fine, but notices a sensor out and instead of doing a limp mode thing just kills it. Not sure how the factory computer handles all that as I went aftermarket.