Show Stopping Knee Pain

Myself and 11 other lads just finished a charity ride upto Edinburgh, we had a day and a half to do this with a headwind for 80% of the ride, rain and even snow at one point so its was quite a challenge to say the least, especially as my biggest distance to date was 40 miles on my road bike. We ended up covering 97 miles on day 1 and 65miles on day 2. Here cometh the problem, on day 2 I noticed pain my left shin and also behind my right knee, as the day went on, the pain in my right knee moved to the outer part of the knee and basically became unbearable to the point were I had to skip a 15 mile stretch to allow me to strap my knee and finish the ride.

I did the ride on a 29er Voodoo Hoodoo Hardtail with road tyres and platform pedals, so I was not clipped in. I felt I had my saddle height correct and also my position from the handle bars all felt OK, I had no back pain and felt quite comfortable, apart from the obvious "ass pain" and leg muscle burn on the hills, is this just down to me getting old (44) I am fairly fit and had prepared quite well with at least 15 rides out of 15 - 25 miles prior to the ride and I also cycle to and from work daily 8 miles per day in all weathers or is this down to bike fit setup? would clipless have been the right option? Any help or advice would be greatly appreciated.

Regards

Darren