2004 Lincoln Town Car dashboard lights

Here's a head scratcher...
I have a 2004 Lincoln Town Car. I have aftermarket HID lights, I had LED turn signal/brake lights, but decided to convert back, but I kept the resistors in and had no problems. I am also running an aftermarket headunit, as well as aftermarket stereo speakers and all LED lighting in the interior.
I noticed with 130,000 miles on the car, the alternator was going bad... No biggie. I swapped it out with a remanufactured, 130 amp alternator... Same as before.
Now, the fun part.
When starting the car and turning the parking lights on, you can see the dashlights, HVAC control lights and clock pulsate.. a little.
Put the car in drive and turn the lights on and it's all FUBAR.
Each time I hit the brakes, the blower fan (if on) will slow, and all the dashlights/interior lights will dim. Turn the turn signal on and I can literally watch it pulsate the dashboard lights AND the third brake light.
The headlights, outside turn signals, cornering lights and such do not dim... just the third brake light and interior lights.
I just purchased a 200am alternator, 70 more amps and higher-output, at the suggestion of a mechanic.
That being said, does anyone have any ideas? Bad ground? Should the alternator help fix my problem? Should I convert back to LEDs??
Please. I'm at a loss.