Hi, new here... I had to reply because I experienced this exact issue years ago. This is probably too obvious an answer, but have you tried shorter crankarms? By my height and frame size I "should" be fine with 167.5s, but I have patellofemoral issues on the bike unless I use 165mm cranks. (Anyone here want a brand new 170mm Shimano 105 triple?) Plus, it really helps smooth out my spin.

I've never had a complete professional bike fitting, but it might be in order for you, since it doesn't sound like your PT has a whole lot of experience in bicycling body mechanics. Obviously seat height, cleat placement and cleat rotation will directly affect your knees, but it's possible that what seems right to you isn't actually what's best for your knees.

When I've aggravated my knees doing other things, a simple stretch before I ride helps a lot. Just kneel on the floor (butt on my heels) for 1-2 minutes to stretch my quads and knee ligaments out.

I overpronate too, and this spring I started working the Chi Running program for correcting my body mechanics, which is doing wonders for me. Just being aware of which direction your toes are pointing when you walk or run - paying attention to how you're balancing your body weight on your feet - is more than most PTs will teach you.

Hoping you're healed up and back on the bike soon.