Regardless, the ECU should not be making any sounds.

Did the setting of the timing fix the problem. I can't figure out if you did that before, or right now.

Are we still dealing with an issue? Sorry, I can't quite figure out the time line.

I would suggest fixing the alternator. It is not functioning properly. Who knows what amperage it is putting out. The engine does require power to run and if there is low voltage (and maybe even less at higher RPMs) it may not allowing the electronics to function correctly.

Good Luck,
Michael

As an aside, and for others in the future, if you are getting code 12 out of an ECU (and the CE light cycles at startup), there is a pretty darn close to 100% chance the ECU is not fried.