If its a ONE WIRE alternator its big output stud wires to the Load (NOT battery/starter) side of the ammeter. Thats where the wire that used to go to BAT on the Voltage Regulator wired, but Id replace it with a new 10 Gauge wire......
If you hooked up Load and Bat and other wires on the old VR wiring you could be backfeeding the coil, I cant say sitting here how you have things wired up now.
Id unhook and not connect any old VR wiring and simply run a wire from the alternators output up to the Load side of the ammeter. Absent any LOAD terminal on an old VR Id wire all loads (lights and ignition etc) to the load side of the ammeter, same side the alternator now wires to. )
If you changed from Pos to Neg ground Id also swap coil wires side to side, you want the coils - to the distributor for Neg ground.