[purple04]

Thanks for not taking it personal. Just trying to help.
Since the problem was after the dealer worked on or near that alt., I'd say there may be a connection. I hate to jump to the "it never did that before" conclusion, but it may be the case here. A good charging system check (pulling the surface charge from the battery, then monitoring the voltage from crank through a minute of high speed operation) should give an indication of what is going on. When an Alt. is upgraded, it can overpower the other components. Kind of like putting a V8 in a Civic. It will idle okay, but if you use the full power, it will break other parts. Your charging system could cause surges through the harness, ground connection, battery cables and ECU that are more than they are able to handle. Running the system with the engine off will discharge the battery, causing the charging system to charge at a high rate when the car is started. This is what needs to be measured, to see if the Alt. is charging over what the system was designed for.
One more thing, this forum is full of tales of ground problems. Check to see if all your ground straps are connected. It might be something simple and common.

Having the dealer rebuild the engine is probably the most expensive way to get the job done. Check into local rebuilders and wrecking yards. There should be a good rebuilt or used engine within 300 miles that would be less than $1000.