I have an Adobe *pdf file from Bose with some techincal specifications and detail on our system. It's not much, but may be of some help. I can't post it here because our site does not recognize *pdf files for download (can that be fixed???). And I can't remember the web link where I found it! Sorry.
But if you will PM me with your e-mail addy, I'll send it back to you.
It appears that all equalization (except the tone controls) takes place in the Bose amps - there is one six channel amp outboard of the head unit and under the dash, and a separate one for the sub. So, if you can get the right connectors for the output of the head unit, you can replace the amps and speakers.
Since we share the same head unit with the Titans and their Rockford Fosgate 6 disc CD changer, you might want to go over to TitanTalk and run a search there. There are some serious car audio fans and experts there posting how they added aftermarket stuff to their system.
I have posted separately on this site some findings from objective testing of the Bose system in my '04 - this is with use of a professional grade calibration CD and sound level meter. With proper tweaking of the bass eq (which has a very bad upper bass cabin resonance in the 80-120 hz range) the system is amazingly flat as it is. Personally I see no reason to upgrade unless one is wanting a lot more power that we already have. Just my two bits.