I agree about the leg comments, you really gotta use them to lean and hold yourself up. You really should just be using your hands to operate the controls and not for holding yourself up. If you have aftermarket clip ons which are below your tripple tree than that will hurt your back (hurts mine), but my shoulders haven't hurt much that I can recall. As far as your hands, sometimes people get cramps in them from having a tight grip on the handle bars (clip ons) and also from braking/using clutch a lot while on twisty roads. For this, a lot of the pros have suggested squeezing stress balls to build up stamina in your hand muscles. I haven't tried it yet but its worth a shot.
ps. i cant believe you got a bike hahaah