There was an "amnesty" for incorrectly registered kits, as long as you had MoT test certs as evidence that it had been on the road in it's present form. I have no idea if that still applies.
The clincher with your Metro will be getting the shell classed as unmodified, sounds very unlikely if you're cutting much of it away to fit an engine in the back. A Q plate will at least allow you to side step some emissions standards.