Absolutely, you do not need to keep all the brands the same. Once awhile some moronic newb will say this, but there is absolutely NO basis behind it. All professional shops use different brands with installs most of the time.
(notice the newb who said exactly this right after me "castmoney").
Ditch the whole bose system. You can start by getting a nice aftermarket cd player, like a pioneer or alpine, and all four speakers. Everything would likely need to be re-wired, as some of these bose systems were tough to re-do without running new wires.
Giving an estimate is tough. If you want one, go to your local trusted shop and see what they say. Beware cheap flea market equipment online. Most newbs make mistakes such as buying junk equipment, and stuff that doesnt work well together (IE getting four channel amps for subs, wrong impedances, etc.)