Don't neglect stretching/moving around when you are *on* the bike as well. I find if I get too focused on my workout or race sometimes I forget to move around a bit as I ride and I hold my head quite stiffly, which causes my neck to start aching. Try to be conscious about keeping your shoulders relaxed and moving your head around every once in a while.
One caution about getting more upright. When I was having real shoulder problems I tried something along those lines and not only did my shoulder not get better - it made my back and butt hurt too....