primetimefishing

My 84 12A had a strange issue occur the other day. As I was driving to work my aftermarket car alarm went off. ( i did not know the car had a aftermarket car alarm) I pulled over and opened the hood. I cut the wires to the alarm horn. upon restarting the car the idle was up and down and a serious power loss occured. Then it just killed. My altenator had been over charging a few days prior and I had not yet addressed it. I replaced the distributor, put a new rotor and now I have a power loss till I hit 4K then it runs better than it ever ran before?
I put a new altenator on and have had it professionally timmed. IT idles poorly most the time and then goes back into tune? Any suggestions?