I had the complication that my MR2 was V6 engine converted but unregistered a couple of years before i bought it. not a problem... just rectify it in the kit conversion process. Did that on both cars actually - not a problem either time. just lost 2 or 3 points in their system, but as everything else scored it was OK.
Just include receipts n photos of the important bits and fill in the simple form. As long as it's clear to the DVLA clerk what has been done and that it's legal, that's all they want to know. Not trying to trick you.