Stereo Whining and constant bass swells

I have a 95 Toyota running dual amps in the trunk, running one 12" sub and four 6/12".  Everything was working fine until I tried starting my car last night and found that the radio and cigarette outlet both were not working.  I checked my fuses the next morning, and sure enough the 20 amp fuse that ran both had blown.  I replaced the fuse, but now, as soon as I turn the car on and even more so when I turn on the head unit, the treble speakers have ALOT of static going through them that whines with and without rpm increases, and the sub has this constant swelling bass.  I am at a loss for this because I tried a ground loop isolator with no success, and I didn't have this problem before having to replace the fuse.  If anyone has any ideas, it would help alot!

Unplugged the RCA's from the amps, and I'm not getting the noises through the stock speakers that are running off the head unit.  I'm going to try moving the RCA's or plugging in new RCA's...but if that doesn't work I honestly couldn't say what it would be.  I'm going to go ahead and take everything apart and check the grounds as well...

Running a Pioneer cd player by chance?Top Secret, I can tell you but then my wife will kill me.

I have run into alot of problems with Pioneer head units RCA outputs messing up. We had 2 cars in the shop last week. If we grounded the outside portion of the RCA, the motor noise and sub noise went away. Solution... stay away from Pioneer. Just had alot of bad experiences with them. Derl