Down payment / Deposit / Reservation fee question

So I am trying to figure out how to set up an initial down payment option for customers. 

I am building a small batch of boxes, I need the customers to put a deposit down and pay the remainder plus shipping once the boxes are complete. 

Example A - Customer wants a box made out of maple, the deposit to get them on the list is $100. The total cost of the box minus shipping is $375 so once I am done building this batch of boxes I need them to be able to pay the remainder $275 plus whatever the shipping is going to cost to their location. 

Example B - Customer wants a box made out of walnut, the deposit to get them on the list is the same $100. The total cost of the box minus shipping is $425 so once I am done building this batch of boxes I need them to be able to pay the remainder $325 plus whatever the shipping cost is to their location. 

So the way I have it working in my head is, I put up the item, limit the quantity to the amount I want to make, once they put down the deposit fee and all of items are reserved I have a list of all the people who put down the deposit and their email, I build the boxes and send out a mass email letting them all know it is completed and they need to finish the transaction by paying the fee + Shipping and I get them shipped out with a return email with the tracking numbers...???

Any help or keywords that I can search or research would be greatly appreciated!

Thanks

Erik

I have the same issue as the OP with the complication of having variants for each product which determine the final price. This makes the workaround above unusable.

 All I seem able to do is require payment in full or ask customers to email if they would rather make a deposit. This is far from ideal. 

Has a workaround I can use or a proper feature been added yet to address this? Maybe it's technically hard, but I'm surprised it is lacking. 

No reply. So I'm infer this is a feature that won't be added. It is important for my business, so next year I'll move on from Squarespace. What a shame. 

@paul2009 Regarding your solution in this thread, now that invoicing is possible with Squarespace could an alternate approach be to send an invoice to the customer for the remainder of the purchase cost once the boxes are ready? If I were to take that approach is it possible to make the physical product (which is the remaining cost to the customer) be a line item in the invoice? It seems I don't even need to create the physical product because line items in an invoice don't seem to automatically connect to store products, but I can type in the product name and price from scratch as a line item in the invoice, although I'd prefer the invoice to know I am invoicing for a physical product from my hidden Store if possible.