Basically there are many times such as the Shannox fight, or if I have a person that really knows how to bust out dps in my group, where they over threat me. I'd salve them and still over threat again, and there are times where they just have to reduce their dps(which shouldnt happen). What can I do to improve this. Also In your opinion how do my reforges, and gems look, I just feel they could be better.
You've logged out in your Ret gear, so no can do on the reforging etc. Your Prot spec seems out dated. you can drop the points in Eternal Glory and Hallowed Ground, and pick up Reckoning and finish off Grand Crusader. Pursuit of Justice is a nice place to dump the final point and even worth taking a point out of Rule law or perhaps Guarded by the Light (if you can't time WoG to get the shield up well) to finish it off. You should definetly Replace Glyph of Word of GLory with Glyph of Shield of the righteous.
using WOg to sump Holy power is kinda dead these days. with the 20 sec CD and removal of all WoG threat its only purpose is as a mminor aid to the healers and as a timed CD to pop a GbtL shield.
Pyrea's awesome guide has nice bits on rotation and is probably worth a read if you're having threat issues