The Bose set up is, Head Unit - Bose Amp - Speakers, so yes, you cannot mix and match your existing Bose system, as Head Unit output levels, impedeance and Amp input are different from the norm, and the speakers are 2 ohms and not your standard 4ohms, so best to start a fresh.
If thinking of a after market set up with amp in the the back, then I assuming your need to run Line Level cables to it, so whilst your doing that and changing speakers, think I would be inclined to do a complete rewire and possibly leave the Bose wiring in-situ so you can always revert back to the Bose set up when you sell the car, or rip out the Bose wiring complete and re sell the Bose set up complete.
As for your Sony HU, sorry cant help there, dont know the model, there are steering wheel adapters available for certain HU's but not all, again for the MID could be possible dependent on HU but your just duplicating info thats already on the HU.
Amp, speakers and subs are all a mater of personal choice and budget, so I think I'll keep out of that one.

Chris.
