Well after literally hours of experimenting and research, I finally solved my AV problems and got the system set up just the way I wanted to.
Since so many people are on this forum looking for the solutions to such specific problems, I thought I would describe the solution I finally found in some detail -- in the hope that someone else might benefit as I have from this forum over the years.
I had a hodge-podge of new and old equipment, and I was pretty particular about what I wanted to accomplish. I have a main TV room where I wanted 5.1 or at least 7.1. I had in-wall speakers in the kitchen and living room that I wanted to drive from my central system in the TV room.
For a main receiver, I was working with a 4 year old Yamaha RX-V2700. I really didn't want to spend the money on a new fancy one, but would have if I had had too.
For inputs I was working with:
Apple TV (gen 1)
Yamaha Ipod Dock
Maingear Gaming PC (which I uses as a 3D BluRay player)
Sony 3D Bravia LED NX720 Internet TV. (BTW, this unit has a ton
Internet-enabled functionality, Pandora, Amazon Movie Rentals, Netflix, Twitter, Facebook, Skype, network access to media stored on my NAS upstairs, etc. I had no idea there was going to be so much when I bought it.)
The first big problem I had is that the Zone 2 and 3 function on the Yamaha RX-V2700 only worked with analog inputs. Since none of the systems I was using was primarily analog, and a few didn't have analog ports at all, this limitation basically precluded using the Yamaha RX-V2700 to drive zone 2 and 3.
So I went down into the basement and found an ancient Onkyo TX SV454. I think I bought it when I was a student in 1993. (I can't believe I've schlepped it around all these years, but now I'm glad I did.) It only takes analog inputs, but did support two zones. So my solution was starting to take shape.
Research on this forum led me to the Gefen Digital Audio Converter, which would take an digital audio optical (or coax) feed and convert it to analog, which I could run it into my ancient old Onyko TX SV454, which in turn would drive zone 2 and 3.
Then I had to figure out how to configure all the rest of the inputs. Here my main insight was that with this new Sony TV, I really didn't need to use the Yamaha RX-V2700 as an AV hub. I just needed it to drive audio fed to it optically by the Sony TV.
The Sony TV has 4 HDMI ports. So I take my gaming PC, my Apple TV, and my DirecTV box and connect them directly via HDMI to the Sony TV. (The fourth HDMI port I use to connect the Sony TV to the Yamaha RX-V2700; as far as I can tell, this is only used when I'm using the Yahama's GUI for various set-up features.) I configure the Sony to output audio optically; and I configure the Yamaha to basically take that optical audio feed and power the audio in the main TV room. (Actually, I run a digital optical audio direct from the Maingear gaming PC to the Yamaha RX-V2700 in the hope that the high-end sound card in the Maingear is doing something for me.)
To get the audio to zone 2 and 3, I need to configure the Yahama to output optical audio via its RECORD function. Put the Gefen DAC in between and presto: any of the audio sources can be played in any of the zones. This is a little inelegant but it worked.
The Yamaha will pass through an optical input as output output, but that it's. (So, the one input device I can't use in zone 2 and 3 is the Yahama IPod dock, which isn't optically connected. But with all the network functionality in the Apple TV and Sony Internet TV, I didn't really care.)
As an added benefit, this configuration allowed me to add two front presence speakers, giving me 7.1 in the main room.
The last piece was to program a Logitech Harmony One remote to make this all work together in a reasonably user friendly way. I'm still fine tuning this, but it's coming together nicely. One thing I wish the Harmony One was better at is supporting multiple zones and amps; setting them up as separate "Devices" is a little clunky.
Finally, an observation about the current market in AV Receivers. I did a ton of research into high-end receivers that could accomplish what I was trying to do here. But what I found it that, with all the functionality and HDMI ports on the latest generation of Internet TVs, most of the advanced features in most high-end receivers were totally unnecessary. 1.4a 3D HDMI passthrough on a receiver is totally unnecessary if you've got multiple HDMI ports on your 3D TV -- all you need is a nice audio receiver
to power excellent sound in your main rooms and in your other zones via a single digital audio feed from your TV. As far as I could tell, there is no receiver on the market that can do that and only that. If there was, I probably would have bought it. But as it is I'm pretty happy that I could accomplish the same thing with a little creative configuration of my Yamaha receiver, a 19-year old amp, and an $80 Gefen DAC from Amazon.
This process has taken me over two months and I never want to do it again. My family thinks I'm nuts and my friends all tell me I should have hired someone to do this all for me. Next time -- if there ever is a next time -- I probably will.
Thanks all the power posters on this forum -- without your reports and expertise, I never could have figured out how to do this.