I'm assuming the bar dips kicked off the tendinitis. But could a shooting binge of .40 in modified weaver aggravated the injury further?
The bar dip's I'm sure were the cause, sounds like you simply strained your shoulder. Shoulder injuries can take a while to heal since you are using it all the time even for the smallest tasks. I wouldn't change up your stance since shooting .40 probably has nothing to do with your shoulder injury. Just take it easy at the gym and go a little more slowly.
I had major shoulder surgery my first year in college. Old football injury I had never gotten fixed that I waited far too long on. About a year later I over extended my shoulder at the gym doing pectoral fly's and could barely lift my shoulder. Breaking down scar tissue is painful and seeing as I didn't take physical therapy as serious as I should have, being in college at the time, this was a result. It took a couple weeks before the soreness went away.
By the way the best thing you can do for your shoulder is slowly and carefully stretch it a few times a day. Try massaging it a bit with Bengay or Icyhot.