You might need a ground loop isolator for your rca's or inputs. You can also ground the radio with a separate ground vs using the stock harness ground or use both.

Check this out...

PAC SNI-1 RCA Ground Loop Noise Isolator - Reviews at Crutchfield.com

http://www.amazon.com/Stinger-SGN20-.../ref=pd_cp_e_0

As for the ipod it probably wouldn't hurt to use one of these unless your headunit controls your ipod.

http://www.amazon.com/Pyle-PLGI38RI-.../dp/B004HJ35RK