I just mean that to make AMR work well with the set-up I use you have to keep setting the Spirit cap higher as your gear scales up to stop it from either giving you pure Spirit gems or too little Spirit. If you feel like you need more Spirit then yes, just trade out the gems, but the main thing that will change your overall Spirit is the trinket(s).
Regarding the Int/Mastery, generally I've found I just prefer the pure Mastery stack in 25 man, where as I put more focus on Int in 10s purely because its more about being able to put people back up ASAP. I couldn't give you a definitive answer on which one you'll find better, but if you go with the socket bonus matching Mastery focus thats a good middle ground to let you adapt to both styles.