89 300e, replaced alt. & now car hardly runs

My alt went out a few days ago and now that I've put a new rebuilt alt in the car, it won't hardly run at all. My ABS won't go off on the dash, an internal fuse in the stereo was blown, and even now that I've replaced it and have power to the stereo, I still have no sound.
I recently replaced one of the fuel pumps, and the car kinda acts like it did when the pump was bad. It won't go over about 60 mph.
Is it possible that the timming was knocked off, when my alt went bad.
Anyone have any advice for me? I'm totally stumped