There are quite a few reasons it may look like a Lightning. The Spitfires had fiberglass tanks (2 or 4 gallon) and that it's quite possible that a previous owner may have had problems finding replacement tank if the original had been damaged or was falling apart from use with modern fiberglass dissolving fuels or simply if it had the US 2 gallon tank was changed for a larger capacity steel one. The Spitfire tanks would have been a lot more expensive than the steel counter parts.
The GP carbs are highly likely to have been swapped out for Concentric
carbs and I suppose it's possible the rims could have been damaged and replaced with steel ones.
Without pictures it's impossible to say how close or far from original your machine is but here are a few items that distinguish the Spitfire MK II from a standard production Lightning.
Alloy Rims of either Borrani or Dunlop manufacture , 190mm front brake assembly, rider folding foot rests, Alloy brake and clutch lever assemblies and AMAL
The genuine mufflers, probably long gone, had a different part number to the common mufflers across the range of the time. 68-2875 instead of the common 68-2733 though there was a 68-2732 also listed for in 66. Good luck finding or identifying those!
As I say it should have the glass tank and the GP 1 5/32" carbs but they are likely to have been swapped out years ago, the engines originally had 10.5 pistons too but that was it engine spec wise.
Hope that helps.
Here's a picture of one I found on the web that's pretty close to an original MK 11 though even this one has had the alloy lever assemblies replaced with the more common steel units. Doesn't have the correct horn. You can clearly see the folding riders pegs and alloy rims along with the 190 mm front brake and 4 gallon fiberglass tank. Even has the GP's!
The breather on the inner timing side cover is of course non standard. I just noticed it also has the 67 style all rubber instrument cups rather than the steel/rubber earlier type.
The GP's were blamed for rough running which was later found to be substandard Lucas