"The only ones I'm lagging behind are in Refine -69/100, Purify -59/100, Rune -43/100, Battle Armor -77/100, Tactics -16/100. This should be pretty good stats."

No sorry, they are not "pretty good" at all. Try getting all of them to a minimum of 80s on all 4 equip sets, except for tactics which Lv3 or 4 will do for now.