I have a questions and several bits of info for you.
1. If you're a caterer (cook for larger events), why do you want to bake small quantities? Unless business is very slow right now, small quantities=lots of work for little $$$. If you're in the latter category, I can appreciate your circumstance. When I first opened, I took anything I could make a few dollars with. Now, after 9 years on my own, I'm more selective. Not because I'm making that much, but you begin to realize that sometimes it's more work than it's worth.
2. I second/third/fourth the Excel spreadsheet. I first learned on Lotus, before there was Windows (it was still Basic when I started). All you need to properly cost your items is to convert to weight as much as you can. Weights are much more reliable unless your dealing with tsp/Tbsp. Also, add in the fudge factor. Prices fluctuate, and since you appear to be in Maine, you probably pay dearly for shipping or 'fuel surcharge' for your food items.
3. If you don't have a book which has equivalences, I suggest "The Cake Bible", by Rose Levy Beranbaum. She has a very good table which has the weights of each item based on a cup (related to baking). Convert your recipes to weight.
4. When you buy your ingredients, create a spreadsheet which will list the item, weight/liquid volume, description, price, date. I date all my items because I may not buy them for a long time, so I'll factor in increases if it's been a while. This will be your reference when putting in your recipe information.
5. Create a 'food cost form' and save it under the recipe name whenever you do a recipe. Plug in the ingredients, cost per unit of measure and yield. You will have the cost per item.
6. As far as a restaurant goes, figure 30% food cost when pricing. Although this may price you out of their ability to pay you and mark it up and make a profit. Look around and see what others are charging for their items and see if you can produce it and sell it at a profit. You have to realize that you may need to sell at 50% cost, but then at 12 muffins, how much can you make to make it worth it?
Based upon your information, this bakery owner probably doesn't want to spend the minimum her suppliers are demanding and wants you to carry her risk. It might put a few dollars in your pocket each week, but what will happen when you're working on a profitable gig and this bakery wants their 12 muffins that don't make you that much money?
I'd be happy to send you a copy of my inventory sheet and recipe form, just send me a private e-mail.
Although, I would encourage you to focus your energy elsewhere. Unless you are making a product that many people would spend the extra money on, manufacturing a small amount of product to sell wholesale is not a profitable venture. That is why mainly large companies produce products for wholesale. And if the bakery buys everything it sells, what are they in business for? If you're going to go to the trouble, you could probably sell them yourself and keep the profit.