I recently ordered two items and remembered to put in the comments box: If you don't have both, don't send any!
I got a very nice call from the store that item b would be in in three days. Did I want to cancel or have them hold the order! That was nice.
I don't remember if you have a comment box but a lot of web sites have a list to check about what to do in a case like that.
Cancel order
send what's available now.
Hold order until everything is available
Send what you have now and send other when it comes in with extra shipping.
Etc.
You could make up something to cover most problems and put it right on the order sheet. I don't know computers but you should be able to make it so the order won't go through unless something is checked.