So I've looked at most of the PTR posts from the front page as well as the gear that was data-mined, and I can't really find any gear that is purchasable by valor. Neither have I seen any mention of new coins for extra rolls in 5.4.
Is valor only useful for ilvl upgrades come 5.4, if you're already geared in ToT raid gear?
Should I be saving Mogu runes? (EDIT: Found my answer here)
They already confirmed there won't be valor gear this patch.
You can use your valor directly to upgrade gear.
There are no new greater charms on the ptr yet (http://ptr.wowhead.com/npc=64029#starts), but if they stay consistent they will let you keep your lesser charms and you can change them into three of the new "greater" charms when the patch hits. No idea what extra-roll charms tot will be using, and what happens to your existing mogu runes. I assume they will convert existing mogu runes to elder charms, and then use elder charms (like in the pre 5.2 raids) in ToT for extrarolls.