It's a difficult one to get any kind of definitive answer on. My personal view is that you are restoring the aeroplane's
identity, which would originally be a 'Mark whatever', although you may in retrospect be incorporating some safety mods which were only found in later marks.
Case in point - I used to be involved on a Beaufighter 1F restoration. Beau 1's had the original flat tailplane, and were notorious for having a pronounced, and often lethal, take off swing. This was also the case with the Merlin-engined mark II, but by the time the mark VI came along, those nice chaps at Bristols had designed a new tailplane with a 12 degree dihedral. She'd still swing a bit, but nowhere near as badly as the early Beaus, and the dihedral made the swing easier to catch and counter. End result - less dead Beau crews, and an aeroplane that went on to become a firm favourite with maritime strike boys over the North Sea, and Aussie mudmovers out in the Far East.
Now, when it came to restoring our Beau 1, we had a dilemma. Build an original-spec flat tail to retain authenticity, or compromise on historical accuracy and do her with a dihedral tail instead?
Safety wins hands down every time. So if and when that particular aeroplane ever flies again, expect to see a Beaufighter 1F with a Mk VI tail.