Another Note: If your engine cranks, and then does not, then the problem is not in your VATS.
It will not crank at all if VATS is enabled and not getting the correct corresponding signal from my experience
You have a crank overheat protection kicking in, a bad ground, ground that is not correctly hooked up, or something else going on.
The ECU could see a signal indicating the engine has started and turn off the crank signal.
Go back and check your harness and make sure it has the required grounding to the block, frame and body.

Post a picture of your ECU! It should have two long plugs on the side (edge) of the case. If you have two plugs on the top, then it is a later ecu and your will need HP
Tuners to tune.