Hard to say what happened now without looking at it. But I fear you may have fried the charging circuit in the PCM. Chrysler computers are very sensitive.
The only other thing I can think of off hand, is that you reversed the "Gen field driver" and "ASD relay output" connections on the alternator harness.
If you do take it to the Dealer or other shop, tell them what you told us...It may help avoid the additional aggravation charge that shops add on when figure out there was operator error involved.
