93 5th Avenue Running Rough - Computer?

93 Fifth Avenue was running fine. Then all of a sudden it starts running rough. When I hit the brakes all lights, radio, etc would go out and it would start to die. When I let off the brakes everything would come back on.
So I change the plugs and plug wires to attempt to address the rough idling and the battery terminals for the other. I'm driving to work and it starts running so rough that it finally died. It will start and idle but idles rough.
I did the on-off thing to check fault codes and got 12, 21, 27, 35, 52. I removed the "computer" and eximined for burn or damage. The next day I put them back and started it back up for several minutes. I checked the codes again and only got 12 and 55. (I thought removing my battery terminals days before would have cleared old codes out).
I took it to a mechanic who determined that one injector was not working right. He replaced it and it made no difference. The injector is getting fuel and the plug is firing, but according to the mechanic it's not firing when it should.
On top of all that, the windows, a/c, and radiator fans are not working (but were prior to all this). Could a bad computer cause all this? Or do I need to continue chasing wires?