It really sounds like a wiring fault, not a component failure. Puff of smoke...
One thing you can check is the grounding. If you lose the field coil ground, (the green from three wire bundle, connected to the REG, on the stock harness) you cannot energize the field coil. Ensure that it is grounded. Check the ground connection to the frame (green wire). Make sure that ring connector is bright, shiny, tight, and the green wire unburned.
Puff of smoke...? You need to find where that came from... scary.
Check the white wire (of the 3 wire bundle) resistance to ground (keyswitch off). You should read approximately 7 ohms on your DVM, through the field coil to ground. Any higher reading is a bad connection. No matter how good everything else is, if you don't read 7 ohms, you'll never get proper alternator output.