I would strongly recomend you NOT add another stereo to the H3. It is pretty much the nerve center of the vehicle.
As far as warranty void... the rule of thumb is, if there is a problem that can be tracked back to something you have changed... you're screwed.
Now, that being said, if you go in with an electrical problem, the techs aren't going to go looking to see if you have an aftermarket exhaust. They are usually pretty cool about that.
