Dunno if your still planning on doing this however, I have retained factory head unit and amplifier/door chimes/etc with the use of the JL Cleansweep. Its capable of using a high level (post amp) input and providing RCA outputs - whilst leveling the sound frequency band over volume. Check out JL's website for more info BUT its more or less a kick a$$ version of an RCA line out convertor.
What Im getting at is not using the new head units RCA's, instead tapping off post bose amp for RCA out, and if re-install of factory system was required, you would have to reconnect 4 channels (8 wires).