Hi,

I think you answered your own question regarding your legs and foot problems. I am not sure what kind of pedals you are using, I am assuming either cages or flats? If you are using flats that would definately make you tired very fast, because you are working only one type of muscles (quads) and not taking advantage of you full pedal rotation. I remember when I started riding last year, for fist 2 months I rode on flats and I could barely ride not feeling rubberish in my legs.
Regarding your shoulder, mimi is right, if you are sitting in front of pc that would trigger this problem, I am saying this because i have this same problem right now in my left shoulder. And I do know it's because of my position in front of pc. I am sitting straight and have to look to my right because my pc is in the right corner of my desk, don't ask it's just how it is. It never hurts when I am hope. Yoga helps me a lot though, try do some if you can. Hope this helps.

FN