The main problem is going to be if you keep your Shaker 500 subwoofers and connect their amp to the remote output on your head unit. The input on those amp's remote turn on from the factory HU is +5v and all aftermarket decks send a +12v signal through the remote turn on. You will need to get a
+5V Fixed-Voltage Regulator 7805 from Radio Shack to eliminate that horrible turn on and turn off BOOM from the factory door subs.
There is a seperate harness, aside from the main radio harness that is used to provide line output signal to your Shaker 500/1000 factory subwoofer wiring. Basically it is a snap harness that converts the Subwoofer out RCA to the signal wiring for the Shaker 500/1000 subwoofers.
As for the nav system, you could always do a toggle switch to ground (with a DIODE if you connect the parking brake wire too), but I recommend that you look to see if there is a bypass for that particular unit. Also, some Pioneers go off of your speed in the GPS program to limit functionality. Once you hit 15 MPH or more, it will lock you out or stop playing DVD video. I don't condone watching videos while driving, but having the nav lockout can suck if you need to make a quick adjustment.