Judging by those legs, I assume you are pretty new to the sport. I had similar issues when I first started out, and especially when I switched to using clipless pedals. A proper bike fit aleviated most of the issues. The other niggles just took time. I think years of doing no sport led to the muscles around my knees being pretty weak. I concentrated on good diet, weight bearing exercise, walking/jogging and miles on the bike which eventually strengthened things up.