Gonna leave this here for anyone who is using.
There is one small issue with the Rune Pouch. To fix it, open up InventoryOptionsHandler and search for:
And change it to:
This will fix the issue with not being able to add Rune's of the same ID to the pouch by using it on them. (This only happened after adding Runes to the pouch, and trying to add more of the same ID to the pouch.) For example, you add 5k Blood Runes, then you try and add 5k more Blood Runes, it would try and say that the pouch is full. This fixes that issue.