Nice review!
One sugestion on your new sub. Try turning the x-over all the way up, and let the Yamaha handle the x-over duties. You'll probably like the results.
Second, learn a bit about SPL meters. They are reasonably priced (Radio Shack about $40 -$50 depending on model) and can make a marked improvment in your set-up/calibration over setting levels by ear.
Enjoy your new system
