I don't have the Bose option, but I'm replacing my head unit too. But I'll help from what I've been reading and from what I'm doing too.
First you should say why you're replacing the stereo. Ist it because you don't like the sound, or you want bluetooth and ipod connectivity? What are you aiming for? Is it sound quality (SQ) or loudness (SPL)?
1 - Depends on the questions above. You can replace the head unit and the amp (or ditch the amp) , or just the speakers. I think you can't replace the amp without replacing the headunit, or vice-versa.
2 - in dash 4" speakers, you have to modify the brackets and glue the new ones to the existing top bracket. There's a world of speaker brands beyond Alpine or Focal. (Focal are a lot better than Alpine, btw) There's a lot of how-tos on that.
3 - They're subs, but probably only producing higher frequencies than the rear one.
4 - You can replace the door speakers with 5 1/4".
5 - You can put a new amp under a seat, behind a seat or in the trunk. Just have to wire it.
6 - I bought the Pioneer DEH - 80 PRS. Single din size the better I've seen is the Pioneer DEX-P99PRS. Don't know about double din.
Have you read this?
link
Hope I've helped a bit.
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