I modded one of my old clunkers (Peavey Raptor I) by putting in a kill switch to cut off power to the output to do some Tom Morello type solo's. Anyway, the switch works fine, but now my guitar sounds muddy and squeals and gives feedback when selecting the pickups and changing the tone. Im not really sure what I did, any suggestions?

Ok, first off, what did you wire it into? Input or return?
It really need to be on the return (earth)
Also, now much did you pay for the switch? A cheap switch will do you no favours

I cut the wires going from the volume pot to the jack and wired the switch in between so it was basically just turning the guitar on and off. It was a 5 buck switch and i used the same type with no trouble in a few effect pedals i built. The switch itself works fine but the feedback is confusing.... like the pitch changes depending on the rotation of the Pots and the pickup selector, so im thinkin it could be somethin to do with grounding?

yeah, but which wire, positive or ground?
It should be in the ground side of the circuit.
As for the feedback, I'm confused. It shouldn't feed back.
There will be earth buzz because of the broken circuit, but I've never encountered feedback when I've done this mod.
I'll have to do some research