Converting my fit from road bike to hardtail
I was really lucky with my road bike fit. It has been dead on with no adjustments. I originally went in b/c of knee issues and they pretty much disappeared after the fit.
I bought a hard tail and the seat tube seems to have the same angle as my road bike. The crank length is also the same. But for some reason setting it exactly like my other bike (except a different saddle) isn't working. The only differences between the two bikes are the saddle (which I adjusted to where it can't be but maybe 2m off due to how much I sink in when seated) and I don't wear clipless on the hardtail. Road bike: feels perfect; MTB: Knee pain again........I really don't get it. Any ideas?
Measure top tube , and try to adjust the stem length to get the reach to be similar to say the brake hood position.
tape measure should help get the mechanics of the fit matched
As to your Knees See a Doctor perhaps one with a specialty in Sports Orthopedics.
Spin low ratio gears.