Edit: clips should be clipless. As an aside, clips is a great way to break body parts if you ever go down in an accident.
Also about clips, float makes a huge difference on knee pain. A few years back I developed the same sort of thing and changed from SPD’s, no “float,” to Speedpay Zero’s which does and within a week the problem resolved itself; it hasn’t ever come back either. Fiddly type of pedals though. Maintenance intensive, expensive, but great for road use.
Cadence, yours seems low if your in the saddle doing that. I climb between ~92-100 rpm. Don’t even think about it; just do it naturally. Sometimes even a touch more. Out of the saddle for a change in position is the only place I’d be caught dead doing 50-60rpm. As the saying goes, “spin to win.”
Seat height, if you’re trying to do a lot of climbing, it can make a difference too. On my “climbing” bike, it’s set a tad bit lower than my other bikes which I use for flatland rides. Drop it by 1/4 cm at a time and do a test ride. The results might surprise you.
Cleat position is a personal thing. Best I could suggest is to make a visit to your LBS and have them set it up. Me? Looking down, I have mine set all the way “inside” the sole so as to have maximum clearance with the cranks because I ride with a “toe in, heel out” style. (Hence having pedals which can float.) Everyone will be a bit different here, body mechanics is a personal thing. Again you’re LBS should have a fitter on staff which can assist you.
Last would be crank arm length, leverage in action you see, but that’s a topic too detailed to get into here. Probably the last thing on the list to change unless you’re on the extremes of a human height chart.