I know that "heel down" sounds funny, and you'll have to think about it in order to remember to do it, but it really works! (with or without clipless pedals or cages or whatever) Other things I've found helpful is making sure my knees and elbows aren't sticking out all willy nilly!

Naproxen for your shoulder -- I've been given that stuff, and find that I bruised pretty easily while on it, so if you're wondering why all of a sudden everything you bump into leaves big marks.... After being told pretty much your same solution for just about all the aches and pains over the years, I've learned to try just that: an over the counter NSAID and ice for at least a few days before visiting the doc -- and generally, it's been a good solution!

Good luck with your shoulders! Mine sometimes hurt after riding too, and then I be more careful not to lean too heavily on my hands, and to relax my elbows! I don't know if that will help you or not, but what the heck....

Karen in Boise