I used to get really sore knees and calf's so I went to a guy who helped me setup the bike. I had the saddle way too low so wasn't getting enough leg extension which was causing it all. Do you have any mates who are keen cyclists and can help set it up?
Generally cycling is fine if your bike is set up correctly and your not over doing it.
I would check your saddle height, AFAIK you should be just an inch or two less than full stretch at the bottom of the pedal.
I am prepared to be proved wrong
front of the knee over the pedal axle when your cranks are horizontal.
I have no idea, if I took a picture of it would you know? (I'll take it tomorrow)
on mountainbikes, generally run the saddle a little lower to enable you to move around on top of the bike, the more extreme the riding you're doing the lower the saddle will be.
Saddle fore-aft is also critical in protecting the knee, as a good starting point you want the front of the knee over the pedal axle when your cranks are horizontal.