Ignition Coil?

Is the starter working now?

If you turn the key to the start position, does the starter turn the engine?

What year are the engines and you NEVER should cut a harness. One may be OBD1 and the other OBD2 try resetting security system ifno manual look online how todo it.

It sounds like you left a ground wire off or the ASD relay is not working. Here is a guide to check the relay and the engine wiring diagrams below so you can see how the system works.

https://www.2carpros.com/articles/how-to-check-an-electrical-relay-and-wiring-control-circuit

Check out the diagrams (Below). Please let us know what you find.

Was the voltage there for the first second after turning on the ignition switch? If it was, suspect the crankshaft position sensor. It should have been removed before the transmission was pulled out, and it requires a paper spacer to set the critical air gap when it's reinstalled.

If there is no voltage for that first second, there's an open fuse feeding the automatic shutdown (ASD) relay.

Slow down; you're getting wrapped around the axle with misleading tests. Your test light grounded the coil of the ASD relay causing it to turn on. That's the job of the Engine Computer. Rather than tearing the Power Distribution Center which can be a pain to put back together, just measure that voltage at the coil or any injector, dark green / orange wire. That's the voltage that comes from the ASD relay when it turns on.

That relay turns on two different times. The first time is that one second when the ignition switch is turned on. It's very easy to miss it with a digital voltmeter because they often don't respond fast enough. A test light does a better job. Since you found voltage feeding the ASD relay contact and the coil, we know that part is okay. If you still don't find that voltage turning on for the first second, we have to determine if the relay is not being turned on by the computer or if the voltage isn't getting to the coil and injectors.

Use the test light to double-check that voltage at the coil. If it's not there for the first second, hold your finger on the ASD relay to feel if it clicks when a helper turns on the ignition switch. If it doesn't click, I suppose we could have a bad computer but that would really be rare. If it clicks but there is no voltage to the coil or injectors, look for a break in that dark green / orange wire.

If you have a tool capable of measuring 25,000 volts safley try checking the coil wire out put, if not it's either the coil, or the wiring to it, or the PCM. Coil is easist and cheapest stating point here, replace and see what happens.

Check for codes first. Also check if htis has a ballast resistor on it that may be bad. Especially if it wants to fire on start but quits when you let off key. Check fuel pressure.