Ok so here's the scoop.

Occasionally when I'm stopping with my headlights on and heat on, my car drops in voltage/power and the lights dim, blower slows down, for a sec then bounces back. Today it did that like 4 times in a row when I was pulling into a gas station. It only does it when I'm coming to a stop and never while I'm driving down the road. The car doesn't really drop in rpms (maybe slightly) so it's not like car is dying per say.

Also, I have a radar detector that turns off automatically after 6 hours. So after I've been driving (like after i got home from work) and park my car, i leave the radar detector plugged in knowing that it will just shut off in a few hours. When I get up in the morning it is off (which is normal) but when I turn my car on, it turns on (which it never used to do). My car also doesnt seem to be cranking as hard as it should. I'm guessing the radar detector is coming on because once the car is running its now getting the full 12v's which turns it on (like as if i replugged it back in). This never used to happen. I would normally have to unplug it and plug it back in so it would turn back on.

So heres the weird part. I know your probably thinking "oh he has a weak alternator or battery". I've replaced both. I put in a brand new optima red top and a 125a alternator. So ive not only replaced the battery, i replaced the alternator with a higher output one and the problem still occurs.

I have no idea why its doing this.

Additional information:

I have a pioneer head unit. I have a alpine 1000w amp and a JL audio 10" sub w/ 2 farad capacitor. I've had the system in the car for a couple years and it never did any of the goofy things until recently. The capacitor always reads really low voltage when the car is off and has been sitting for awhile. Like low 10's. Sometimes its so low it wont even be on.

So heres the question. Why is this happening? Is there something that controls the voltage output from the alternator? Could I have some unknown draw in the electrical system that is draining constantly?

I could pull the fuse on the stereo system but I don't think its going to change anything.
I have also cleaned up all battery terminals and cleaned up all grounds.

This is really starting to piss me off and would appreciate any information or help that you could provide.