head lights pulse after bypassing my bulkhead

Hey Kit, I thought about the diode idea, but this does not seem likely to be individual pulses. The alternator is spinning faster than the engine by 2x or 3x and if this shows up at only high RPM, the pulsing would be at a rate of close to 100 pulses per second with 2500 rpm form the engine; the headlights would not respond to that rate of pulsing (nor would our eyes!).

I would suggest to the OP to:
1) Try a different VR is he has one ===> OK already done.
2) Turn off and on things like radios and the blower to see what effect this has
3) Look for any filter capacitors in the car's wiring; on the back of the alternator is a good spot to look.
4) Try disconnecting the original alternator output wire and have just the new wire from the alternator output to the battery; I don't see where you disconnected the original wire...??

Also, questions to the OP:
- Is this flicker fast, like many time per second, or slow like 1 or more seconds per flash? That might help us figure this out.
- How old is the alternator?
- How old is the battery? (It may not be a good 'ballast' any more if it is old.)