I take off any extra fuses if the radio is already fused in the car at a fuse box, since there is no need for another inline fuse when the line is fused @ the box and at the back of the radio. The only radio I've seen that doesn't have the fuse built into the back but on the constant power is the newer alpine deck that doesn't have the cd -player and is meant for I-pod mostly.... Otherwise if a deck had a transformer of some sort on the constant line, I leave the in there as well, so your little image there, I personally would of cut out the fuse, but left the transformer in there, obviously the manufacturer put it there for a reason, I don't know what the reason is, but they wouldn't spend the money to put it there unless it was suppose to be there.... IMO....
Here's a test, but try unplugging the RCA's from the 4-channel and see if you still get whine, maybe there is an internal rectifier or something out on the amp itself, if that doesn't affect it, try getting someone to hook up some temporary RCA's that run outside the car to a different radio and see if the whine stops, I'd say your best course of acting is to just start swapping out things until it starts working right, you may even want to try a new radio and see if the whine stops.... Have at er man....
I'll try playing again tommorrow.