I was recently working on my friends 99 Sunfire with the same passlock issues. Intermittent starting, Theft Light on, fuel system dissabled, etc.
I was running thru the relearn sequence when I stumbled across the solution to the problem. I had the key in the run position and tilted the steering wheel upward to get out of the car, upon doing this I heard the fuel pump kick on and the theft light went out, so I turned the key and the car started fine. Then I shut it off, tried it again and it started right up again. So I started to think that maybe it was related to the postion of the steering wheel. I moved the steering wheel back to the down positon and sure enough, the car wouldn't start and the theft light was on again. At this point I decided I needed to remove the steering column shrouds and find the cause. After removing the shounds, I turned the key to the run position and tilted the steering wheel up, and again the fuel pump kicked on and the theft light turned off. I found that the cause of the problem was the ignition harness didn't have enough slack and the connector at the left side of the column was being pulled outward (not completely out) every time the steering wheel was tilted down, and then pushed back into place when the steering wheel was tilted back up. I zip tied the connector to hold it in place, tested it with the steering wheel in all positions, and now it starts everytime without the theft light coming on.
Thought I would throw this out there as another thing to check for when dealing with this dreaded Passlock system, and THEFT Light.
Good Luck!