Thank you for all of the ideas and insights! I did some more testing last night. I used the paper towel tube method and verified that the tweeter is working. In fact, I covered the tweeter and four woofers with my hand one-by-one and could tell that part of the sound was gone with each. So, it seems that the speaker itself is probably working fine. Everything was brand new and I never abuse my speakers, so I just wanted to rule out that the speaker was defective out of the box. Also, I re-checked the wiring yet again.
I re-ran YPAO several times and each time the sound was similar. So, it's not a calibration issue or at least not an issue that I can fix automatically (might go back to manual tweaking later).
Now, what I think is happening is that the center channel might be overwhelmed by the two fronts. The large dual 8" woofers of the R-820Fs just have much more presence in the large room than the quad 3.5" woofers of the R-34C. I can compensate by bumping up the gain on the center channel, but playing a test tone on each even with the same sound level (measured with the SPL) the left and right channels just sound more substantive to my ears.
The other thing that just occurred to me -- the center channel is too high. Sadly, when I was building my house, I neglected to think about where the TV and speakers would be located when designing the rooms. The floorpan is very open so the only location for the TV is above the fireplace (I know, it's not ideal and I never thought I would position a TV so high). The center channel is flat on the mantle which means that it's actually pointing one or two feet above the seated ear level. I'm going to try and get some larger rubber feet for the back of the center channel speaker so it tilts forward, pointing it at ear level in the seated position. This probably will be the most impactful change that I can make.