I got my MS-8 replaced and re-installed. Aside from the gripes I had mentioned earlier, it is working quite well. As others have mentioned, it nearly ignores the underseat subs so I found improvement by increasing the those frequencies associated with those frequencies.
I did come across something that had me worried for a while. When I turned the subwoofer volume higher (The separate one not associted with the MS-8 at all - just the one on the sub amp), I would get a disconcerting popping out of channel 1 (MS-8 channel 1). I thought it might have something to do with the proximity of the MS-8 to the sub (about 5") but that didn't make much sense - even if I am driving it at 1100 watts.
Since I had been retrying different scenarios on the acoustic calibration, I left the microphone plugged in and the mic was left in the trunk with the sub. When I disconnected this, the popping went away. Problem solved.