I am not surprised that the Emotiva doesn't add anything. The Yamaha should have enough power for Klipsch (which are known for their efficiency). Having the Emotiva just ensures power definitely is not the issue.
I have a friend who bi-amped his RF62II and he thought there was an improvement, but the fact that he thinks it and doesn't know means we are not talking a major difference.
I think of the Klipsch as the most "punchy" speakers among what you might find in your local B&M stores. The 5" drivers really should be able to perform well enough since you are offloading the bass from your mains! Double check that your mains are not running full-range. I don't know Yamaha's terms, but for Denon, the speakers need to be set to small and the subwoofer mode under bass settings should be set to LFE+Main (you can check to make sure the sub is playing when you listen to an audio only source like a CD. This would ensure the sub is set to play the low frequencies from the "Mains").
The fact that your center (with 4" drivers) passes muster is perplexing. I really hope the leads on one of the speakers got reversed because that would make better sense of it all.
Next time you run them, also feel the air coming out of the ports in the rear of the speakers (I think two per speaker IIRC). It should be roughly equal from all of the ports. On the left side, the ports are firing into a pocket. I don't believe that is an issue, but it is easy enough to pull it about 12" in front of your console as a test to see if there is any change.
Have you tried Pure Direct yet? This eliminates almost all processing, so rules out many factors that might cause the problem.
Evaluating your system before you mentioned any issues, the sub stands out as the weak link. Swapping your sub would definitely be money well spent. But I'm not sure it would fix your problem, so hold off if you don't have money for new speakers until we run our of options. You don't want to buy new speakers only to find out some snafu in the setup caused the issue.