I could walk, hike, etc. for miles on end but biking was killing my knees. I worked with a PT PhD and it made an amazing difference. One bike fit session fixed it. She hitched my bike up to a indoor bike trainer stand and watched me ride. Then she adjusted my seat, my handlebars, and directed me through postural changes.
I don't know where you are located, but I highly recommend it. Just did a quick google search and found this place -
https://www.velofitpt.com/bikefit - might be worth a try.
Also - how are your IT bands? I biked throughout the PNW hills during my years in college and beyond, and really had to work on my IT bands so that they wouldn't pull my knee caps out of alignment and cause pain. A sports medicine Dr @ Georgetown helped me out then during a visit back home.