Are you riding on a bike that only has holes in the stems, or do the bikes have micro-adjustments?
I have been intructing for 10 years and am on the short side (a little over five foot tall), but have a problem if the bikes don't have micro adjustments.
If I were setting you up, I would probably set the handlebars a little higher than you're used to riding with on your outdoor bike, and move it as close as the adjustments allowed.
Of course, I'm saying this without seeing you, but it's been my experience that the clients that have shoulder issues do better with a higher setting on the handlebars.
I hope you can resolve this issue. Indoor cycling can be a great way to stay ahead of the game when it comes to your outdoor cycling.
Vertically challenged, but expanding my horizons.