if it's the former, you can go have a fit done to get the best you can out of the bike you have. If you're all the way down in an aero position, your knees shouldn't be coming that close to your elbows. As far as the nut pain...sounds like your saddle may be nosed up or you're too far forward on the saddle. Your perenium is taking a beating...that can be a function of anything from a bad bike fit, to a saddle that's not for you. Man, I would STRONGLY recommend having a fit done. There are different levels of fits. The best ones have you bring in your shoes. You clip in and they take video of your pedal stroke from all angles. They do a ton of measurements and try to get you in the best position within the bike's limitations. Most even adjust your cleats properly.