Originally Posted by
BengalCat
If you can do barbell squats and they don't bother your knees but the bike does than you can be 90 percent sure your knees oar OK but your bike fit is not.
With your measurements, a custom-built bike MAY be your only solution. I know of one person with similar all legs and a short torso and that is what he had to do. (I don't know about his arm length.)
Good luck on being able to modify a stock production bike to meet your needs and knees.
The OP hasn't answered my question about the location of the knee pain. Thus all this discussion is academic. Without knowing that, it's impossible to give sensible advice.