Speaker setup
Chad,
The Yamaha auto-setup is great for setting the speaker distance and SPL level, but sometimes you have to tweak the other settings. It sounds like you don't have a sub and your mains are full range, so LARGE would be appropriate. Make sure that the center and surrounds are set to SMALL, sub to off, and a crossover of 80 Hz would probably work well.
If you add a good sub from SVS or HSU, you might find that it handles the LFE better than the mains and set them to SMALL to enable the crossover.
Also check the Parametric EQ setting and compare the system with EQ ON/OFF. Experiment with the settings and enjoy the HT.