Its like I can see the alternators current waves in all the lights.. Why is this? Bringing it off idle seems to help? I'm not to sure
Sounds like the voltage regulator. Also could be a grounding issue.
^ This. Could also be a sign that your brushes aren't in the greatest of shape, but I since they're integral with the voltage regulator you're really replacing both and it's immaterial.
Mine did the same thing and then I swapped with a spare I had and it fixed it. I'd say get a new regulator and brushes and you're good to go.
Now that I thought about it more, in the end mine was so bad the EGT needle started bouncing around.
In the car I could change how fast the lights pulsed by revving up or down or turning different electrical loads on and off. Then I tested it on a real alternator test stand and it passed with flying colors, I couldn't adjust the load, the machine somehow just made it charge at 15A at 14.7-9v. I never got that high of voltage with it installed.