OK, here's the breakdown if you're interested. I have two commuter bikes; I have a bike-train-bike sandwich commute, with a 4 mile ride each way. I cannot take a bike on the train. Both bikes are locked up for extended periods of time (one is locked up every night at the stop near my work). The bike I put the most miles on, by far, is my recreational bike, which I would never lock up as it would get stolen in probably 1 h. The commuter bikes are complete junkers that I fixed up and made ridable. One I actually found in the garbage. You'd have to be insane to steal one, along with the fact that I use 3 locks on each. What's funny is I'm actually concerned people will see all the locks and think of it either as a challenge or that the bike is more than meets the eye. Both commuter bikes are traditional platform pedals, while the rec bike is SPD mountain clipless.
So, long story short, it would be silly to spend a ton of money to get fitted on a junk commuter bike that probably isn't causing the issue (just aggravating it) and doesn't get nearly the mileage my rec bike does.
Anyways, I see what you're saying about PT. But here's the issue: I know I have some biomechanical problems as running has always hurt, the PTs told me so, and I've had various biking issues over the years that resolved from strengthening/stretching; the knee injury described in this post as the exception. There's no question in my mind that I need to fix the biomechanical issue, but I wonder if fixing it will change my specific bike fit.
I have actually explored the internet and found a bunch of recommendations for a fitter. The session runs about $325, which seems really steep to me, but maybe I'll just bite the bullet. Does that seem reasonable?