Generate a bill from an item receipt instead of the PO?

Some of our PO's have a hundred items or more and some of these are shipped on numerous shipments.  If we receive a half-dozen shipments against the PO over a couple of days then attempt to generate the bill from the PO after the group has been received, we find all items from all item receipts to be merged into the automatically generated bill. 

The vendors have generated invoices which match their shipments, and we therefore need to bill in the same groupings as received (and as invoiced). 

For small orders, this is simple, just remove a couple line items and save, then bill again, remove a few, save, etc until each bill that needs to match each invoice is done.  This is wildly more difficult if a hundred items have been received on a half-dozen receipts.