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Ok, I didn't notice you had mentioned the smoke and burnt electrical smell previously... Wow, did I actually miss that? Check wiring too, more may have burned than than the ECU. The ECU is pretty well closed up, actual smoke is more likely to present from wiring or a relay. Do you know that you jumped the wrong pins? If so which ones? One big issue with burning wire harnesses is that the wire doesn't always burn to the point that continuity is interrupted, you often get shorts across other wires where the bundle is wrapped tightly together... not fun to track unless you can narrow it down by locating two devices which are not both operating and share the same harness.

No need to buy another M/T ECU, the A/T ECU should function the same. I'm pretty sure there aren't even any wiring changes to be made.

The fuel mixture would have to be obscenely rich to prevent the engine from at least chugging for a minute after a cold start. Especially if it's been allowed to sit long enough for the excess fuel to evacuate. I'm talking rich to the point that the injectors are leaking. Now, that said, it might behoove you to pull them and test them as specified in the ECU to be sure they're not leaking and are opening when voltage is applied. The shock of the combustion in the intake could damage injectors but I don't think it's very likely. If you think the cylinders are flooded then pull the plugs, crank the engine for several seconds and let it rest for 24 hours to ensure that the vapor has had time to evacuate the cylinders.

The electrical components in the two AFMs are identical and present the same scaling when tested in the same housing. They are completely interchangeable. The housing swap generally requires tuning. I do not recommend using the air bypass screw for this purpose. Its scope is full spectrum and the airflow signal needs to be tuned selectively for the best performance and to ensure that you're not creating any lean spots or washing a cylinder. Do yourself a big favor and invest in a fuel controller and a wideband controller. The wideband is an invaluable diagnostic tool. Innovate Motorsports makes a couple very inexpensive controllers that are very well rated and easy to use.

A boost leak isn't going to cause a problem like this... You'd have to have a 1" or larger hole in the piping to see something this bad. A leaking BOV won't have any affect on the operation of the engine when not boosting.

You haven't made any modifications to the AFM or sprayed any type of cleaner on the sensor, have you?

I haven't gone back through the thread yet and it's been a long day. I will try to make time tomorrow. Hopefully we can get this sorted out in the next couple days and have you on your way. Open and inspect the old ECU as you said. If any of the traces or components are burnt see if you can identify which pin(s) on the harness are related and thus limit the amount of time you may need to spend diagnosing the wire harness.