Flickering or pulstating Headlights

Headlights are flickering at idle and while driving.
Not just headlights really but headlights, tail lights, dash lights.

My setup is as follows.
Newly installed 5.9 Magnum, with serpentine setup and '99 magnum alternator.
New battery
Voltage regulator appears to be solid state type.
Madd electrical ammeter bypass was done at the same time as the engine swap.

With the old 318, and before the madd bypass all I can remember is the lights would dim at idle, and brighten when raising the rpm. Don't remember them flickering, but its been a while.

I'm no electrical genius, but pulled out my volt meter and checked a couple things.
Battery with car off is reading 12.65 volts.
Battery with car running at idle is fluctuating between 14.25 and 15.25
At the alternator output stud, about the same 14.25 to 15.30
The alternator seems to make a little kind of whining noise, just for a second, every time the lights flicker.
So flickering lights and I think the charge rate is a little high, and fluctuating
Any ideas ?