Well I really appreciate the help! but that is a lot to try and figure out lol.
But I did find a way to over ride the json in a way(Don't really know if this is overriding/over looking the recipe.json).
I just had to make sure the recipes were the same.
ItemStack recipeOutput = new ItemStack(SicmishItems.dough, 1);
GameRegistry.addShapedRecipe(new ResourceLocation(Reference.MOD_ID, "dough.recipe"), null, recipeOutput,
new String[] {
" ",
"S ",
"FW "
},
'S', net.minecraft.init.Items.SUGAR,
'F', SicmishItems.flour,
'W', net.minecraft.init.Items.POTIONITEM.setContainerItem(net.minecraft.init.Items.GLASS_BOTTLE)
);
Again thanks for the help!