Hi Kander16, I can try to help clarify some things with the new 1.12 recipe formatting:
As far as I know of with the shaped crafting recipes go, you are only allowed to 1 shape per .json file, thus requiring 2 files assuming you still want those same configurations.
Also for the shapeless recipes and the id's of the materials used. I experienced this as well but I had to change it to if I had more than one of the same thing I had to repeat the entry instead of using the ["count: X]; however, because Forge 1.12 is still in the early works, it's possible this could or couldn't change.
And as for the last one, I can't help you there as I've never messed with the OreDictionary.WILDCARD_VALUE too much. But I hope the rest helped you somewhat!