Shorter cranks helps a bit, more upright position will probably just move the problem elsewhere unless you have
very restricted mobility elsewhere (Hips/lower back).
For pedals, just get the earliest time ATACs that you can find (if you want retro).
Think the very first Aliums are *just* old enough, and the design stayed almost the same for 5 or 6 years. So even the later ones still look fairly retro. Plenty of smooth, almost free float.
I've got one very explodey knee, and have done since i was 18 (big crash), was told i'd need a knee replacement before 30. Now well into my 40's on the original knee.

No sign of any major problems yet either.
So the other thing to do is see a doctor/physio and do all the exercises they recommend. Plus a bit of massage, ITB is very often the entire cause of knee issues and is quick and "easy" to fix. (But can be extremely painful for ~30 seconds!)
Have had issues with some pedals with small bodies, the shoe can roll off the end of the pedal body while still clipped in and make any knee issues far worse, so that rules about 80% of the pedals on the market out!