Hey Ed, I think that's spot on. Really take some time to position your stem, handlebars, post, and saddle. If you don't know how to fit your bike to you get some help.
Sore shoulder could be from obvious things like your bag or how you slept too.
Otherwise thinner rims tend to be less stiff I believe and can soften the ride quite a bit. Also don't under estimate vibration. Getting good bar tape/grips and/or gloves can stop your nerves and muscles in hands, arms, shoulders, and upper back from over working.