Alternator not working after upgrade

The VR power supply/ sensing wire is spliced to the "run" wire somewhere up there near the ballast resistor. You likely cut it out of the loop when you put the MSD in there. Hard to tell just what you did.

A late model alternator (starting in 70) has what is called an isolated field, AKA the brushes are both insulated. The blue to one field terminal on the alternator must have switched 12V from the "run" circuit, as well as the VR ign terminal. The VR has a green feeding to the remaining brush on the alternator, and that controls "the ground" of the field to control charging rate. Pull the VR connector, and the blue off the alternator. With the key in "run" and the engine stopped, both the alternator field blue and the VR blue should show battery voltage