I don't have any experience with aircraft engine repair, but I do know that if you're ever not happy with an invoice, request a more detailed breakout. If the shop quibbles about it, let them know that your next stop will be the local FAA office, followed by taking the engine to another shop to determine what work was done and what parts are new, ensuring all parts are certified, etc, followed by a call to your lawyer to recover teardown/inspection costs from the shop that gave you such a questionable invoice to begin with.
For that matter, if they give you a hard time, make them show you THEIR invoices for the parts they put in your engine, and let them know you'll be going to the part manufacturer for lot numbers in case the engine fails early. Again, if they argue, let them know the next folks they'll be talking to are the FAA and your lawyer.
The last time I discussed acft maintenance with my civilian flt instructor, he said that the FAA doesn't like A&Ps who cut corners or do shady repair work. If they gave you a bill that was unexpectedly high, you need to demand a full accounting of all repairs including a very detailed breakdown of parts and labor. Hopefully he won't hold your motor hostage for payment but if he won't tell you what he did to it, then do you really want to hang it back on the plane?