i would spend an extra $200 or so and get a clarion head unit that way you wont have to deal with any of the drawbacks of the bose system. Also, you could save money on just getting a cheap pair of speakers for the rear since they are pretty useless in a vert. and if you get the headunit you wont have to purchase any of the bose interfaces.
You can get a 2 (or 3 channel amp if you want a sub) for the fronts, run the rears off the headunit's amps. and probably would end up spending close to what you would spend if you didn't replace the head unit.
My plans would be as follows:
Clarion cd/mp3 Head unit (try
www.carmedia1.com) ~$200
Jl audio 3 ways (can be found on ebay for ~$380)
Pheonix gold, soundstream, eclipse, jl audio, or ppi 4 channel amp to power the fronts and a sub ~$350 ( bridge ch 3&4 for the sub) with out a sub you could probably find a 2 ch amp for ~$250
10 or 12 inch sub and box ~$250 or save a $150 and build your own box.... let me knw if you need plans
cheap rear speakers or none at all ~$90
This isn't going to be a killer system but i think you would be really happy with the sound and the price
one last thing, you could save money on the front speakers (and get a less powerful amp) if you didnt go with a 3 way, but they are sooo cool and sound great!