DW, although you didn't fully describe the TV and cable box, if you're indicating that the component output from the box is HDTV and that the TV is just standard definition, then the presence of component inputs on the TV doesn't necessarily mean that the HDTV will be displayed. The TV would either have to be HDTV or down-convert HDTV to a form that it could display. So, there's probably nothing wrong with either your connections or settings.
As to YPAO, let me suggest that there's a good chance that you can keep the dogs and three-year old quiet for the few minutes necessary; your wife may be another matter.
If I follow, you now have just the M60s without a sub, so no calibration other than the M60s would be involved. You should certainly also run the room equalization. From my experience about a year ago helping a colleague to set up his 2400, I'd suggest that you try the "low" equalization rather than "flat" to give a little more adjustment to the mid and upper bass range where it's more needed. If any break-in was necessary, it took about a couple of minutes rather than a couple of months, so don't worry about that.
