ChipSeals

Congratulations on your ride.

#2 could be any number of things but you can't diagnose it without a fit session. (Or maybe, without providing photos to people versed in fit on this forum.)

Limited to my own experience:

— Sore shoulder blades are due to too long a reach to the brake hoods. (Note that I said brake hoods, and not handlebars. You flex a great deal when you brake.) This can be remedied with a shorter stem, shorter reach bars, or a shorter frame reach.
— I sometimes will get a sore shoulder if I ride in the drops too much.
— Sore undercarriage can be due to too much perineum pressure from the saddle. Check your saddle angle and make sure that it is not angled up too much. Most people find the best fit with a level saddle, or with the nose angled down 1-2 degrees.
— You might need a saddle with a cutout, especially if your bars are below your saddle.

All that said, riding long distances is a bit of torture to the body. We're not designed for it. No amount of fit will remedy that. You can compensate with technique: varying hand position and your position on the saddle, taking frequent breaks, making sure that your shoulders are relaxed and your back is neutral, and of course — building your core and your cycling technique.