Thank you for taking the time to post today, Ed.
Technically, you can still create an invoice even if QuickBooks warns you of having a zero quantity. However, this will result in a negative inventory count, but it will be adjusted when you build the assembly. This will also result in having an income for the sale of something that does not exist.
Instead of giving them an invoice, you can give them a sales order listing all the items they paid for. Then, you'll want to enter a message in the CUSTOMER MESSAGE box pertaining to their payment. You can also give them a written acknowledgment receipt of payment if they request for it.
Please let me know if you have other questions about this.
By the way, we have blogs relevant to our situation today. Feel free to check them out.