I have started to use the game booster application Razer Cortex which allows a user to turn off processes, services, and what have you before launching a game. It is a lot like AlacrityPC in that regard. Also, I have begun running the MSI Afterburner app to overclock the video cards. This has eliminated nearly all issues, except the pause-and-play issue. The Razer Cortex was especially handy in trimming down all the apps that share dat, update in the background, and do other things that may cause the foreground stuttering issue. Using Afterburner just helps to make sure the frame rates don't dip in the heavier wooded sections.
What I found is that you can push the overclock of the video too far, which doesn't cause an issue with the cards, but can cause things like the AH3 water to flicker even worse than the cloud shadows do. However, overclocking also eliminated the cloud flicker, or HTC adjusted something, because the flicker is gone now and the sun shining through the clouds causes a change in lighting intensity. I much prefer that.
The pause-and-play issue is causing flight to lack fun completely. Takeoffs and landings are especially prone, as are engagements. The point at which you have a firing solution will see one nearly every time. The only thing I have left to try is moving voice off to a second system, which will eliminate using in game vox and is obviously not an ideal solution.