I'm sorry, I just don't understand what you're actually doing based on what you said, which is why I'm struggling with an answer. Are you charging for the cutter or not? From the calculations you're showing above, it seems like you're instead deducting the cost of the cutter from the cost you normally charge for cookies, and thus cutting into your normal margins on the cookies. That just doesn't make sense to me - you should be charging for the cutter if it's a one-time use specific to the order.
Also, for whatever it's worth . . . you can definitely compute your actual materials and labor costs - all food service business (that stay in business) do.