Try searching this subject on the road bike forums as well...

But I think if your knee hurts on the outside of the knee (knee cap area) then you will want to adjust the hieght of the seat. If it's in the back of the knee then it may be the fore and aft positioning of the seat (ie move it forward or back some).

As for foot pain... I had a similar siiuation and I needed to move my cleat back a hair as the ball of my foot was just slightly ahead of the center of the spindle. Adjusting the cleat back helped to line up my foot with the spindle.

But as everyone said, everyone is different so try adjusting things one at a time to see if any one thing helps or doesn't.

If worse comes to worse, go get fitted by a good bike shop. They'll be able to dial in your position for a pain free ride.

Good luck!