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For reference, according to AonE's translation of episode 131, Itachi tells Sasuke: "If you awaken it, there will be three people, including me, who have ever used the Mangekyou Sharingan."
That's all the info we have. We know it is not Obito because as you said, he died just after gaining his sharingan. Kakashi might have developed Mangekyou shortly after the Kakashi Gaiden and just has not used it (or has been unable to use it effectively) until the chapter he uses it in (haven't read it, just going off of what I've heard). It's also possible that he only recently developed the MS during the 3 year gap, and the 3rd user Itachi referred to was either someone who lived long ago, or someone who has yet to have been revealed to us.