Another way to accomplish this is to create a Sales Order rather than a job, at least for the stocked inventory items.  Each item goes on the SO line with a zero selling price.  Associate the job number to the SO, and it should appear in the Job Profitability report once you create the no charge invoice to the customer from the SO.  Of course, you do not send this invoice to the customer.  An additional nicety of this activity is that all of the quantities you put on Sales Orders will also show as Allocated Quantities in your inventory item screens.  This can be helpful if you want to maintain a certain stock of of some commonly-used items.