Before you spend more money upgrading your bikes, you should go get fit to your bike. John at Cutter's Bike Shop fit my mountain bike to me back in early Spring. I just went back for my follow-up on the MTB and he also did the fit on my 'cross bike. He uses the Specialized BG (Body Geometry) program. He does a full physical appraisal and then goes to work on fitting your bike to your body. With some cleat adjustment and using shims in the foot bed of my shoe he corrected a pedaling issue I have had since my knee surgery back in 2008. He spent a lot of time getting my seat height adjusted properly. I have experienced considerable approvements in comfort on both bikes. If you are serious about improving your comfort and performance on your bike, I suggest you go see John Ronca at Cutter's and get your fit on!
BobK