cyclezen

fitting a mountain bike is diffferent from road. And it also depends on kind of 'riding' one does.
But pain in the front of the knee and with over-engagement of the Quad usually comes from too low a seat.
And usually seat setback combined with seat height becomes a relational thing, but the more vertical seattube/post angles puts more emphasis on getting a good seat height for the gears you ride (and terrain).
Work on getting the seat height to a place that reduces the knee and quad pain.
If you're running typical mtb tires - slightly to more deeply lugged, you're not going into cadence ranges which might commonly be used for 'road' bike cycling. But if you can;t be in a gear that you can hold a consistent cadence, then use the next lower gear or until you can keep the cadence up and steady.
MTB fit can vary quite a bit, depending on the terrain you're riding - a lot depends on what position/posture your bike is providing in the current setup...
not something to cover in a couple paragraphs...
MTB Frame size - could fit in a wide range, I could ride a Sm thru Xl, if I could find a seatpost long enough to set my seat height in the smaller sizes... LOL! some riders do fine on small frames and like the quickness in technical terrain. Others like the feel of long and low. and that will also vary by wheel size. Frame size is likely not causing your issues.
work on the seat height until the knee and quad pain reduces and maybe becomes commensurate with the riding effort.
Ride On
Yuri