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Where's the pain located and what triggers the pain in terms of leg movement i.e. flexing, extending, rotating legs internally/externally, standing on the leg of the problem, or is it a pain under stress like jumping, running, stairs, sitting, etc.

I don't if relevant but I remember trying natural glute ham raise and flexing and extending causes patellar to move so doing the natural GHR caused patellar to move and then weight over the exposed knee join leading to bursitis and I couldn't sit or stand without pain, so I had to just rehab it, re-strengthening the muscles to sit, stand, then box squat and forward step downs off a box, etc.

Knees hurt only under stress and not by much. But if i play bball, the next day they are swollen and hurt more. Its not debilitating or anything. But i cant run full speed or consistently play bball anymore

I had xrays done, i think i may need an MRI. The physical therapist i went to years ago said it’s either an MCL issue or a meniscus issue. I’d like to get a second opinion

I think i need an MRI but boy they are expensive

So it wasnt a single jump, but you’re right that it happened after a long layoff.

I didnt play bball for about a year but kept lifting. Squat got up to the 400’s. Came back and played a high intensity full court game. Next day left knee was swollen, but painless. Didnt think much of it. Next week played another full court (swelling had subsided already). Painless. Day after that both my knees swelled up like crazy and i could barely bend them halfway

Today my right one seems worse than my left

Pain isnt in the tendons. 10 years ago it was, strengthening VMO and foam rolling IT/hips took care of it 100%

Now the pain seems to be inside my knee or something. Like at the bottom of the femer, below the kneecap? Top of shin bone? Its tough to pinpoint

Ill have to try leg extensions tnite to see if i get pain

usually tendinopathy takes more than just release work and stretching to fix, since the tendon itself gets damaged, and takes many months of gradually higher, long duration loading from ISOs and slow tempo quad work to fix. Shallow angles to start so the tendon doesn't get compressed against the patella as it will be swollen from the injury.
And stop loading it while you do the rehab

This is a sound progression, but you can use other exercises like leg extensions which isolate the problem area
https://www.jump.science/2020/12/jumpers-knee.html

Sounds more like patella tracking issue you fixed.

If the pain is below the knee cap then it's most likely a meniscus damage or the cartilage on the bottom surface of the knee cap.
Need an MRI to see which.

Meniscus damage on the outer side can heal naturally , but inner damage won't, due to no blood flow

Yeah cartilage likes compression and relaxation cycles.

So start walking more, which has helped me a couple of years ago, along with the backwards walking up a slope.

I think I have some cartilage chip off the back of my left knee cap, which the MRI I had never showed....
I originally got my MRI for a possible meniscus surgery, but the knee specialist surgeon said mine was fine with even some fat inside it for lubrication - even after years of hard jumping on concrete.
But I had clicking/pops and pain in that knee from the cartiledge catching in there once in a while... which one of the female assistants pointed that there might be damage there but the doctor ignored it...

Soft tissue work and stretching did eventually fix the patella mistracking that caused it, and then that period of walking and backwards walking did the rest.
But it was originally hurt on one jump I took after a multi year break from BBall, where I was fat, poor mobility tight and weak muscles, and years of sitting on my ass.
It still clicks and pops when I do quick unweighted leg extensions, but no pain, and not every time.
And I can feel a "bump" when doing it slowly

Lesson - don't jump when your out of shape! And ease back into it.
Body does not like valleys and peaks, keep to a steady upward slope of stress increase.

walks do not need to be long, I'm thinking like 15-20 mins, but I would wait till your knees settle down first

Every area of my quads, outer, inner, top , bottom,
glutes and adductors
calves and tibs
foam roller wasn't enough I had to use harder balls and rolls

couch stretch, hamstrings, calves/ankles, glutes, piriformis, internal hip rotation

like the above video showed, you need to fix every area

It was a lot of work, but how much do you want it?