Rotator Cuff  

Unless it affects your ability to safely do the job now, hold off on involving the AME.

Get it diagnosed, surgery if needed. "Self-ground" with short-term disability until you're released for work by PT/ortho.

Return to work and report it with documentation from your ortho at your next FAA medical exam.

That is the procedure. For your peace of mind, the FAA is primarily interested in conditions that potentially result in immediate incapacitation. Joint repair isn't one of those. Your AME will just watch your range of motion, ask if you're having any problems, and issue your certificate. Call AOPA's medical section if you need assurance.

(Just in case you need to hear it, Army rules aren't FAA rules)