This is what I am doing for now and I'm getting pretty good results.
I purchased a Hauppauge HD PVR 2 1512 and connected it to the Directv Genie with the included component video cable and adapter and analog stereo cables. The Hauppauge is one of the few devices that I could find that will capture HD. Using the included ArcSoft Showbiz software I am capturing the programs that I have previously recorded and saved on the Genie as I play them back in real time. I am saving them as .mp4 files which I then run through VideoReDo to cut out the commercials. VideoReDo has an 'Ad-Detector' that automatically scans for and cuts out commercial breaks. After editing, I can play my files with my BoxeeBox. The quality seems excellent so far. Pretty happy overall. Thanks for all the help.