I had a Bose system in my 95 Camaro that I put an aftermarket deck on, I remember there was an extra adapter that was like $70 that was needed to make it all work. The sound quality was never the same and I ended up replacing all the speakers and adding an amp.

 

Seems to me if you are using the speaker level output from a head unit, and you use unchanged stock wiring, you are overloading the amp/speaker modules, that are expecting a line level input. Based on my "home" experience with audio systems, distortion, and eventually burning out the Bose amp or the speaker would appear to be a natural consequence.

In this case, if the passenger side rear speaker works, but the driver side speaker isn't working, the rear amp has power, but there is a problem with either the driver side wire from the head unit to the amp, or the speaker has been burned out.

Plus, the wiring for the Bose system is very light gage because its dealing with line level power, and isn't intended to carry speaker level power. Sounds like a recipe for disaster.

 

Yep. ^^^^^^^