another comfort tip for you to try when riding low on the bars is to rotate your hips forward and flatten your back. That may put more unwelcome pressure on your man bits, or maybe not, it's up to you to try. I find that I can hold a "lower" position much longer that way, as opposed to the hunchbacked approach I used to take.
Other than that, evaluate your saddle height as a start. You can flip through this website if you're bored... it has some good stuff in there.
http://www.cptips.com/knee.htm