So...you couldn't register a Saab Sonett or an RD400 street bike ?
I never heard of a 2-stroke ban. Bummer.
I'd get all my paperwork in VERY GOOD order and give it a go. If that clerk had a problem with it, I'd go back another time, or to a different office, and try again.
Friday afternoons are usually a good time to go. And...the busier they are, the better.