I just wanted to make sure you were using the same ECU. For the 96 there's the Fenix 5.2 Motronic 4.3 and 4.4. I don't know what the 6.2 is...
Lets see, if it stays running then something isn't telling the main relay to shut off (or the relay has gone bad). When you pull the ECU, if you are leaving the battery connected, you have to wait until the main relay shuts off power (usually within 2.5 minutes of turning off the engine.) The relay's on the fan shroud on the battery side.
You say you can get no codes from A-2, but can you run diagnostics? With the key in Pos II push the button 3x, it should test a bunch of components, including the relay.
What happened to the previous engine?
I'm also wondering if there's a problem with the car realizing its off. I can't remember if a faulty ignition switch would do anything like this however if the ECU thinks the car is running, it won't turn off the relay (and therefore keep draining power). I don't know why it would keep one thing (the IAV) on but not run the other (fuel injectors)..
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If you're not driving it "like its stolen," are you really driving?
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