OK, new strategy. After all of the above it became clear that M40s are the way to go, but I don't want to drop the $$ today until I get a bit more of my new house paid for (or at least get the old one ready for sale).
Part of the problem was that I had my megachanger on the upstairs system, so it was the place where all my music was accessible. The downstairs system just had the DVD player and a small stack of CDs.
For the short term, I think I'm going to pick up a new DVD/DVD-A/SACD player (probably the pioneer 578), move my existing Sony DVD player upstairs along with the stack of CDs and move the megachanger downstairs with the big AV receiver and the M60s.
Won't improve the bass response upstairs, but will move all the bass content away from the upstairs system
The only remaining "imperfect" is that I currently have the Atoms pulling surround duty in the basement and M2s upstairs. The Atoms don't seem to match the M60s all that well, but maybe some crossover tweaking (get the crossover up above the mid-bass hump) will help that. Worst case I move the Atoms upstairs but I really do prefer the M2s there after direct A/B testing.
Medium term solution will be some QS8s in the basement.
Thanks again guys.
