Knee pain during full flexion

Hi. I'm hoping somebody can help me find a diagnosis for my knees.

I have visited multiple physiotherapists and orthopedics but none have given me a clear diagnosis and answer to the cause.

MRI shows the following -

Left knee: Grade 2 medial patellar chondromalacia, focal oedema at superolateral infrapatellar fat pad, and patellar tendinopathy at the tibial attachment.
Right knee: 6x3x6mm pericruciate cyst posterior to the PCL, superolateral infrapatellar fat pad impingement, and biceps femoris tendinopathy.

Symptoms:
-Feeling of fullness at posterior of knees when near full flexion, significant immediate pain (feels like my knees will explode) during active full flexion (as in sit squatting), delayed pain (a day later) at various points around the knee during passive full flexion (as in when using hands to pull knees in);
-Soreness along right knee MCL inferior to the joint line after repeated hamstring stretching;
-Both kneecaps more sensitive to slight bumps at times
-Used to have pain going up and down stairs but subsided after I stopped weighted squatting
-Was painful running but has improved after cessation of weighted squatting

No pain on either knee during prolonged sitting. No stiffness during inactivity or after waking up. No pain along joint line on either knees. No pain during full extension of knees. Can partial squat with weights with no immediate pain.

Can the knee pain from deep flexion be caused by infrapatellar fat pad impingement? I know it's typically associated with pain during full extension, and I do have slightly more mobile knees (able to straighten slightly past 180 degrees). Multiple medical literature state that there is also significant pressure on the infrapatellar fat pad at greater than 100 degree flexion but I have not seen much discussion online with regards to infrapatellar fat pad impingement causing knee pain during flexion. If it's not fat pad impingement causing the pain then what is it??

Thanks for any help!