Thanks for the info everyone!
My mechanic finished replacing the alternator, however the convertible top is still not responding. He also replaced the "reaction rods" for the top, as I guess one was damaged with the top tried to open on its own.
My mechanic seems to be at a loss as to why the top won't open, however he said he thinks the computer needs to be "Re-sequenced". Does this sound right to anyone?
He said I will have to take it to the dealer to have this done... I'm less then excited about a dealer trip after just doing $2200 in repairs.
My concern is that I am going to pick up my baby in the morning, get half a mile down the road, and have the car go crazy again. I just can't wrap my head around an alternator having caused a temporary computer problem, and it only effected the convertible control programming.