As you probably saw in the identification tables here on the Forum, the engine, trans, and frame prefixes should be EQ, GB, and YF respectively. V2D sounds more like an inspection department stamp (V5 was very popular.) However these were always stamped in fairly small characters, like 3/16 of an inch high.
Douglas was not unknown to assign special prefixes to one-offs. However I have not read anything previously that indicated they had done this for Fulton's machine. By all accounts it was a standard machine off the line, that Fulton had modifications done to by the factory for extra carriage capacity, sump protection, and such to make it more suitable for the rough conditions expected. Possible, but I don't know. V2D is completely outside of the range of any engine or transmission prefix known to be assigned.
As you probably know from the story, originally it was equipped as an outfit, but this was written off in a crash in Belgium at the start of the world circumnavigation.