If you're going to replace the deck, speakers and put a new amp to the speakers...what are you asking? At that point you would be bypassing the whole Bose system. If you're talking about using the Bose amp to drive your components, I don't think that will work. IIRC, the Bose amp has built in crossovers and whatnot, so you won't be able to just hook it up to different speakers. I would just bypass the whole Bose system.
2002 Pontiac Bonneville SSEi
Pioneer DEH-P6000UB head unit
Alpine SPX-17REF 6.5" components (active)
Sundown z15 (3 cubes @ 35hz)