Game automatically eats food I don't want to eat. Also has wheat listed as an edible item which i'd like to change but I have no idea how.

Doesn't seem likely that this is caused by AppleCore. What other mods do you have installed?

I've got pams harvestcraft and hunger in peace but when by itself, pams wont allow you to eat wheat and such

Can you post your full mod list? Have you tried removing only AppleCore and Hunger in Peace and seeing if wheat is still edible?

Automatic eating, as in eating something you're holding instantly with a chomping sound is a vanilla feature/bug. Though can't say what's making wheat edible.