So I ended up getting a Giant Anyroad 2 in February:
https://www.giant-bicycles.com/us/anyroad--2-2016
I trained up for a 50 mile charity ride for work and was doing great all the way through the event, but started experience awful knee pain in my left knee on subsequent rides. From what it sounds like from other riders and googling, maybe my quads got much stronger than my aducters and hamstrings so my knee wasn't tracking right. Does that sound normal? Usually the pain hits when it's bent about 90 degrees.
I've been rolling out my IT band on a foam roller and doing stretches and squats with my feet pointed out to try to balance it out. I rode for about 8 miles today for the first time in a couple weeks and didn't have any pain, so it sounds like I'm doing something right. Any other advice? I really felt it when I was riding in high gears up hill and pushing hard instead of pedaling faster. I've got crank bros egg beater pedals tool
A few things:
If this was your first time doing any form of long distance you may have just over trained and thus you had the knee problems. I once over trained so bad my quads felt constantly tight for almost a month.
The muscle imbalance you read about is not going to happen this fast, it will happen over time.
"Patella femoral" is a catch all name for what your describing but it is not always muscle imbalance as you're targeting. It could be, and very likely is, just you being REALLY tight in the hips.
Stop foam rolling your IT band because if it's inflamed you're just going to piss it off even more. Foam rolling is like a massage and should not be a replacement for stretching.
Chill on the squats, you may not even need them. In fact this could even be making things worse
Stop pedaling in super hard gears, thats not how you get better. You're only going to aggravate everything even more
Did you make sure to get a bike fit? You can do 800 things but if you're bike is not set up right you're only going to be going in circles.
You felt fine because you didn't do anything for a few weeks so your muscles likely recovered.
Look up stretches that target your hip flexors, hamstrings and glutes. Also look up core activities like dead bugs, press ups, planks, hip bridges. NO CRUNCHES