Something like this would have to be almost completely custom. Were it me, I would create a new page similar to orderconfirmation.aspx, that would only be shown to customers who have purchased a product with the upload later option, and then show them that page instead of orderconfirmation.aspx. The new page should have the same information as orderconfirmation.aspx in addition to the option to either upload the files right from that page, or be taken to a page where they could upload the files. You'd have to make sure that you have the order number and order kit cart records to make sure the files get uploaded and tied to the correct orders.
<a href="http://www.aspdotnetstorefront.com">Shopping Cart Software</a>