Can I add a 4 channel amp to the system, bypassing the factory equalizer and amp? I want to leave the sub the way it is. I've already replaced the 4 door speakers. My main goal is to get read of static and the overdriven highs.

 

The weakest link on the stock TL bose system is the sub. You'll be surprise how much better the overall sound will be if you replace the sub and add an amp to it. But to answer your question, yes, you can replace the amp. You'll just need to get a high-low adapter and convert the signals to RCA so your new 4 channel amp can accept the signal.