So I'm back for my one-week update:
I've been testing my hypothesis that above all else, the hips are key to addressing my PFPS problems and so far the results have been excellent. My program has been very simple (so I can religiously keep it) - two or three times a day I will do side leg lifts, clams, mule kicks, and fire hydrants. I'll roll for about 15 minutes a few times a day. This is in addition to my usual light core work and yoga (power or barre) once or twice a week. I've mixed in some simple VMO work, but it has not been my primary focus, as I really think my VMO development is fine due to the barre yoga.
After three days completely off, I've been able to pick up more or less where I left off and ride pain-free. I've been able to do a hilly 20+ on the MTB and up to about 30 miles on road with no issues provided I keep up on the program. There's no doubt the bike fit has been crucial also, and probably even the leading factor in recovery so far. Needless to say, I've been surprised with how quickly I've responded to the exercises.