There is a box on the registration form 8050-88 that has a box you can check that says the airplane was built from parts. (see the link below) That might be the way to go in this case. I would run it by the DAR that you are going to use first though. He will be the guy who says yes or no in the end. JImChuk
Microsoft Word - 805088Paul.DOT (faa.gov)