I am trying to solve this problem too.... came up with this...
To allocate inventory to lump sum per quote jobs.
I invoiced the job as usual "Total Per Quote $40,000.00" and presented it to the customer for payment.
I then created another invoice listing the inventory parts and quantities totaling $8,000.00
I created a discount item called "inventory discount" that is "non tax" linked to my sales account.
I enter $8000.00 to remove the increased sales created by the inventory asset moving to the COGS Material account and there by increasing my sales account on this invoice.
I have another discount item called "inventory sales tax discount" that is also marked "non tax" linked to my sales account.
I enter the amount of sales tax $800.00. This now makes my invoice zero 0.
The way to think about it is that technically the customer already paid this invoice in the lump sum per quote amount. The customer will never see this invoice. You moved your inventory from assets to expense and hit the profitability report for that job. AND the sales tax is waiting for you to pay in your Sales tax liability account.

This is how we are going to do it.... if you see any flaws please let me know.... all my testing seemed to affect every account the right way.