I have a '96 3.8. After completing an engine swap, I tried to start the car but the security light was on. I tried a different key and it worked. I ran the engine a couple minutes and shut it off. I didn't try to start it for another couple weeks because I decided to take out the transmission and rebuild it. I got it all back together, but the car had the security light again and wouldn't crank. I tried the resistor bypass, nothing. I got the pulse generator and hooked it up to the pcm, grounded the theft deterrant relay, and now I can get the car to crank reliably, but not start. When I crank it, I can see exhaust coming out the pipe, so I know it's somehow firing, but it doesn't want to start. The only thing I have observed is that the idle bypass valve sometimes seems to go haywire. I can hear it clicking open and closed even without the key in. I figured maybe the car isn't starting because it's stuck closed, but I get the same result even if I hold down the pedal while cranking. I'm pretty much at a loss so any help would be appreciated. Thanks.

 

Most likely what you see coming out of the exhaust is vaporized fuel, which could mean that the injectors are working, but the ignition might not be.

 

I'm getting spark at the one coil terminal I checked... I suppose I should check the rest though. The exhaust did smelled burnt, not sure how well.

 

While you are at it, you may want to look at the plugs & see if they are fouled or wet with fuel.