We are having trouble finding the least cumbersome method to transfer and account for the products we make and purchase that are in our inventory, but then are removed and used within our business.

For instance, we remanufacture toner cartridges and a customer may purchase their toner, paper, and various other office supplies from us, however, we also pull items from inventory to use in our own daily business, either in our Quality Control/Testing department or through plain old admin/front office.  

The purchase order for the incoming items is coded to the various GL accounts for COGS or Inventory and are processed through the IPR account.  However, sometimes during the receipt process, but more often after the fact, the items are pulled for use and we've had to do a list of crazy, disjointed, and disconnected entries to reduce inventory and move the costs from COGS and/or Inventory to corrected general ledger accounts.

We've done the "Issue in Inventory Control, then move the GL costs in a journal" processing for our remanufactured items, but items are often missed or the costs are disconnected from the issue entry and things get missed or messed up.

We are currently playing with the idea of issuing zero cost Sales Orders to ourselves, "receiving" then creating zero invoices.  However, then as a last step a general journal created to move the costs.  Or possibly creating a debit and credit memo in Accounts Payable if an invoice for that product is outstanding to move the costs. However, we are worried about having to calculate the differences in the FIFO cost entries sent to GL when the zero AR Invoice is generated and the actual costs for that inventory item.  In addition, we are worried about our sales margins be skewed throughout the month.

Any suggestions and/or examples on how other companies deal with similar issues would be greatly appreciated.