[JLMounce]

H pipes have a propensity for drone, especially with straight through style mufflers. A rule of thumb I learned from my late model mustang days was that this combination generally mattered.

With an H-pipe, run a chambered muffler like a Flowmaster
With an X-pipe run a straight through muffler like a Magnaflow

I have the Pypes 2.5" system with X-pipe. Originally I had the Violator mufflers and there wasn't any drone in this system but it was just very loud everywhere. I replaced the Violator mufflers with a set of Magnaflows. The car is now pretty quiet while cruising around in the city, or even on the highway, until you get into the throttle, then it wakes up nicely. There's absolutely no drone anywhere.

If you're not currently doing so, make sure you are running full tail pipes as well. Dumped mufflers will create a higher propensity for drone as well.

[Lifetime Goat]

Epilogue on this thread.
I replaced the Dynomax muffler with Pypes Turbo mufflers and 90% of the annoying resonance is gone. I still get a little at a very specific RPM but all in all I am happy with the result.
Thanks to all those smart and experienced people who commented.