1988 Other Chrysler Models Charging System

I have a 1988 Dynasty that used to have a 3.0L engine in it. I put a 2.6L Mitsubishi engine into the car. For 2 years I have not had any charging system problems with the car until this summer. On a road trip the alternator called it quits and I had to run on straight battery until the next town, which killed the battery. I replaced the alternator, battery and continued on with seemingly no problems. I noticed that at idle the volts jump all over the place and all the light flicker. The heavier the electriacal load the worse the flicker. My first thought was the regulator. The alternators that were used with the 2.6L had internal regulators in them so I put in a known good alternator with no change. Is it possible that when I lost my alt on the highway that some wire started to carry an electricial load that it was not designed to carry and in turn it burned? And now it can't do it's job properly anymore? I have noticed that if I hit a really good pothole or bump the charging system will be fine for about a day.

P.S. This a carb engine therefore there are no computers onboard. I took these out when I changed engines.