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fried ECM when checking coils?

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Wife's engine was running rough. when I disconnected the ignition wire from cylinder #1 (rear left when looking at windshild from the front bumper) I found no change in engine performance, indicating the problem. Stupid (STUPID!) me, I went to plug the ignition wire back in with the engine still running... and used a long metal implement to guide the plug back to the terminal (impossible to access this one with hands/fingers!). There was a little spark when the metal implement touched the plenum, then the car died instantly. When I plugged in my scanner, it said it could not detect the computer! Engine cranks but does not fire. So, I figure I fried the ECM? I ordered a new one (used). Are there any thoughts out there on what else might be the problem in the meantime?

Before replacing the ECM, I plan to talk the plenum off and change the plugs and coils in the rear. I will check the insulation on the harness wires as well, and hit any with liquid electrical tape as needed.

So, what else can I do to screw this up? from what I read, the ECM will need to be flashed by a dealer before the engine can fire... aside from doing this after I get everything back together, what are the chances that the engine will not fire again? Will I miss something else that might have also been damaged by the short circuit?

Thanks!

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