FUBAR Gear

I'm trying to empty my bags to give me plenty of room for MoP levelling junk.

I notice several things.

a) A lot of my Holy set have red strength gems in them?  WTF???

b) I have upgrades to various sets in my bags, gemmed, enchanted & reforged yet they are not the piece assigned in equipment manager????

c) Best of all, I'm in Pearlfin Village in Jade forest and there appears to be a vendor that sells upgrades to almost all my gear :)

This is going to take some time to sort out ...