Has anybody had any experience removing the whole Bose system and replacing it with something more conventional?
Good quality modern headunits are relatively cheap, as are half decent speakers. Rather than chucking a load of cash at trying to repair the Bose system, would it be viable to change it?
BOSE speakers are an odd impedance .. if you change the headunit you also need to change ALL the speakers as well, you also have to either forgo the steering wheel controls or find a patch lead that works .. 
Plus if you have a NCDC HU in there rather than a 2006 would also mean loosing your On Board Computer Info as well.
I would go for a fix first, plenty of Omega Bose bits kicking around out there and a lot cheaper than going for a complete rip out, re fit and a shit load of rewiring if you want to retain a Sub Base system in a complete new set up.
Out of the 8 speakers in there 4 of them are in the front doors, so pretty unlikely all 4 are blown, more likely to be a wiring or connector issue in my opinion. Audio Amp wise feeding the speakers, there are low level Amps in the HU which in turn feeds the main Bose Amp located at the rear of the car which then feeds the speakers. The Amps used in the system seem to be fairly reliable tbh, unless totally abused.
Think if it was me, I would rip one of the door front door panels off and see whats going on in there, in case its been played with in its previous life.