Lights dim, speakers cut out when braking, turning on/off headlights, etc

Vehicle information:
2002 325Ci with Harmon Kardon sound system, upgraded head unit (OEM, 2005)

The issue:
The speakers cut out and the headlights dim when I press the brakes, roll up or down the windows, turn on and off the headlights, turn on/off windshield wipers, and turn on off turn signals. It doesnt happen every single time I do these things, but ranges from occasioanlly to frequently. I've tried extensively to figure out the problem, but no fix so far.

What I've done:

• removed fuse for head unit (lights still dim)
• swapped head unit with another e46's (no change)
• Removed fuse for headlights (speaker still cuts out)
• removed fuse for brake lights (no change)
• removed fuse for "thiefproofing system" (no change, attempted since it was an aftermarket add on)
• Removed fuse for cigarette lighter (no change)
• removed fuse for front windows (no change)
• unplugged trunk amplifier (seemed to decrease the frequency)

Additional information:

• My alternator and battery were replaced last December, and did not have any effect on this issue
• My car seems to hate the ignition in 2nd position. This issue starts to happen almost every time I mess with any of the instigators. Sometimes the sound will stop altogether until I turn the car all the way on. There is also an occasional electrical pop when I mess with the instigators. I have been unable to pin point where the pop is coming from.
• I asked this on a forum almost a year ago, with less information, and someone suggested unplugging the battery leads and shorting them together for 10 mins. I gave it a try, and surprisingly it solved the problem for three months. I started having problems again, so I did it again and it worked for another three months. However, now that "fix" has no effect.

If anyone has had a similar issue and fixed it or have another idea of something to try or test before I bring it to a shop and give them ridiculous amounts of money.... please speak up!

Thanks