From my reading so far, a separate pre- with HT bypass is likely to provide the best improvement in 2 channel SQ(?)
Absolutely! Putting a stereo pre-amp in the mix will definitely improve your 2 channel listening. It has been my experience that the 2 channel pre-amp sections in most AVR's are merely an afterthought. And this is where the refinement will come from - the pre-amp.
Since Ricred1 has the same speakers you have, it would be wise to listen to him. I think his Parasound separates are a terrific choice and offer a lot of performance for the money. The P5 pre-amp may be a good place to start and it also has HT Bypass.
Don't forget that there are many high quality integrateds with HT Bypass too. This is the route I took in order to reduce the amount of components in my installation. And I really couldn't be happier. Good luck!