Thank you all for taking time to write your responses. Just to give you all a quick update, I'm back at square one with the system and the calibration. what I mean is that I will be resetting the SC-95 back to factory specs and restarting the calibration process tonight. Here is why:
Last night I stopped in at a local audio shopin Lake Grove named Audio Den. I went there hoping to get to listen to one of their home theater rooms but unfortunately the room is getting renovated. Instead, I was treated to an audition of a the Wilson Audio Sabrina speakers which were powered with a preamp and amp combo from Moon audio. Needless to say, they sounded awesome, but my biggest take-away was being able to listen to what they consider a to be well calibrated setup (albeit 2 channel stereo). So I went home and fired up my setup and listened to the same songs that were auditioned (a few from James Blake including one called "Limit to your Love" which will test your speakers bass capabilities). As I listened to my setup both in 2.0 Stereo mode as well as 2.1 Stereo, I Instantly noticed that something was not quite right. I went back to listening to the 2.0 because the sound was SO different I couldn't believe it. So I decided to go back into the MCACC PRO settings to review where the settings ended up after the last calibration. I noticed that the mid bass frequencies had being EQ'd much lower than the others, which could explain why I felt that the mid bass punch was absent. I then activated one of the MCACC memory settings that had not been programed, which would result in the AVR removing all of the calibration and playing in its natural unaltered state. To my surprise (and relief) this made a world of difference, as I could now hear the fullness in the music that missing. I sat back in my listening chair and enjoyed the sound that the 2.0 stereo setup was now producing. Of course it didn't have the lower bass extension that the Sabrinas have, but I'm ok with that, since the Sabrinas alone cost close to $17,000 for the pair, and the the Moon amps probably another $10,000.
This whole thing is bittersweet since I've reconfirmed the fact that I can get good sound from my setup, but I now have to systematically re-calibrate the whole system so that it can sound good for music as well as movies.
Now that I have research and experienced the capabilities of the MCACC PRO calibration program, I realize that there are a lot of different settings and adjustments that can be made but should not be left at the sole discretion of the FULL AUTO SETUP. My plan is to continue to read and test the effect of each of the settings, and hopefully arrive at one that gives me the best sound for my setup.
Thanks again to the gentleman that posted the link to the MCACC thread. If only there was a summary page that explained everything without having to go through through the 5,000 posts.