Hey Ryan,

I’d start by looking at whether you are able to fully externally rotate your arm. A lot of times your dominate side does a lions share of the work in these movements and if you aren’t able to fully stabilize your shoulder, you’ll end up with pain. Here is a good vid to start with:
http://www.mobilitywod.com/2012/12/open-and-closed-torque-systems/

Followed by parts 1&2 of this vid:
http://www.mobilitywod.com/2011/10/episode-330-the-muscle-up-receiving-position-the-organized-shoulder-part/

http://www.mobilitywod.com/2011/10/episode-330-the-muscle-up-receiving-position-the-organized-shoulder-part-2/

Good luck