I'd start with some basics here. The
Phoenix had the front cockpit, twin nacelles, and missle body. Maybe incorporate the old Vulcan ring drive in the back of a missle-like body, or a centrally fixed section the nacelles attach to with rotational sections fore and aft of there. Or mount the saucer vertically and spin that for "gravity" with nacelles attached to the center axis, and maybe a bridge structure attached ahead of the saucer where it could act as a lifeboat.
I'll draw out some ideas on lunch here quickly to show you what I mean.
(edit: very rough, but here's the illustration to give you an idea of what I mean. Personally, I like the rotational sections the best with the Vulcan drive ring second.. but the centre saucer idea could certainly be explained with early rotational gravity simulation. Use what you like, or nothing at all.. no worries either way.)