Follow up, some of the basic things I couldn't get to work:
1. Surround speakers. Using the optical digital audio link from the DVR, I was able to get the front speakers and sub to work, but no surrounds. There are references in the manual about using the surrounds for a 2nd room, but I couldn't figure out how to configure or unconfigure it.
2. Connected progressive scan DVD player to component video inputs, no picture.
3. Connected same DVD player to S-Video in hopes of seeing it and configuring it, no picture
4. I tried repeatedly to get the test tone to work so I could troubleshoot the rear speaker problem and couldn't get it to work. Finally, I tried it one more time and it worked. I have no idea why.

Now that I write this all down, I guess I didn't get 75% working after all.