The determination as to whether the CT Luxury Sales Tax rate applies to a custom job is based on the final selling price of the piece. There is no differentiation between parts and labor. When processing a Custom Job transaction, you must check the Tax entire sale as if it was one single item checkbox found by clicking the Sales Tax drop-down in the lower right of the POS screen.
This means that custom jobs should be processed on their own and should not be mixed with other transaction types.
You must have the system option Item Tax - Treat As Single Sale enabled to see this checkbox at POS.