You should only feel obliged to pay for any work that is done that has moved your project forward. Any time he put in the body is a wash at this point so that leaves what he's done with the neck.
The plek is questionable as to whether it'll work out for a different body so I am not sure I'd commit to paying for that. If he installed tuners or cut a nut for you, that is really the only work that would be chargeable IMHO.
