In response to the "duplicated" thread, in Problems, I tried to make a plugin that, when an item is clicked (InventoryClickEvent) the plugin checks if the itemid is part of the Not Allowed To Be Stacked List
int[] notAllowed = {310,311,312,313,
298,299,300,301,
302,303,304,305,
306,307,308,309,
314,315,316,317,
272,273,274,275,
276,277,278,279,
283,284,285,286,
267,256,257,258,
290,291,292,293,294,
261};
And if the amount is greater than one, simply drop the items individually at the player's feet to be picked up naturally.
I failed. Paradox, if you could possibly handle this, please do. Unless yall can think of a better solution.