Over the last couple of years I've put a couple of thousand painful miles on my trail bike. I prefer road riding but hot, windy weather had kept me on the trail. It was painful because no matter what I did I couldn't seem to get the fit just right and my knees would ache after every ride. I played with saddle height, handlebar height, hand position, cleat position etc. I couldn't make that sucker fit.
Currently my bikes are stored in the dining room on a rack that has 1 bike over the t-bike and one across. It was while looking at the trail bike while contemplating a ride, I noticed something a bit off. The saddle was almost 2" further back than on my road bikes. "Gosh", I said, "funny I didn't see that before." I don't know how I missed it because once I saw it, it was pretty obvious. I have to say that is one adjustment that has made a big difference. Of course, I still prefer the road but I no longer dread the trail.