If you aren't having fuse blowing problems anymore-

And your only problem now is that it won't run on automatic-

Then I would look for the processor "run" light on the CLC. If it ain't on, you might have bent a pin on a eprom, or put one of them in off by a socket hole. Did you take pics before yanking the proms? Is there another car you could look at to compare? Do you have the right power supply voltage coming into the processor board?

The last time I got involved with that, we had long sockets, with spaces for many more pins than there was on the chips. The question became, "Do we sqaure them up with the top end of the socket, or the bottom end?". Unfortunately idr what the outcome was. I think we compared it to another car.