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I think I would pull out the plugs & put an inspection light in & look around, maybe a nut fell in the intake.
I would also take off the flex plate & crank pulley to be sure a bolt wasn't hitting.

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I'd be taking a peek in the holes and if nothing there, call your engine builder. What all did you do to it when you got it home? Did your guy do a complete build or did you finish it up? I would'nt try to reuse a standard type head gasket. There are gaskets that are reusable tho.