Here's what I'd probably do if I was in your situation.
(1) Buy the Clarion deck. Forget about Sony. It'll break right after its warranty expires.
(2) Move the separates up front (if you're happy with their sound) and get the Boston's out of there. Components can handle more power, will sound better, and will create a much, much better front soundstage.
(3) Get some decent speakers for the rear deck (6x9s right?). You can easily find something acceptable for $75 or less.
(4) Get everything hooked up correctly. I'm assuming you've got everything running off the single set of pre-amps off the alpine. It sounds like you're headed in the right direction with the 3 sets of pre-amps, so go with it. Just make sure that your amps are getting enough power. You might want to consider 4ga cable going to an 8ga distribution block if your exceeding 500w rms in total.
(5) If your amps don't have x-overs, get some. Don't send your speaks frequencies they can't handle. I'd hit the front components around 100hz, the rears around 60hz, and the subs around 80hz. But, those are my preferences, so experiment to find the ones that you like best.
