I believe there was a reason Elijah (a) was seen with Moses (a) and Jesus (a). Elijah (a) never died, and indeed, Jesus (a) was saying, just as John (a) was killed and people are denying Jesus (a) now, there is always a person holding this position, but Elijah (a) will not be manifest, but hidden, for reasons, that if he was in the open, he would be treated like John (a) and Jesus (a), and Jesus (a) wants people to know he will return one day but he is a light in the world so long as in he in this world.
The prophecy regarding Mohammad (s) is clear by Jesus (a) if you keep in mind the holy spirit is a position held by all chosen ones, including John (a) and that there is always a leader on earth.
I think disciples understood the comforter in the future to be Mohammad (s) and the immanent one that will be sent by Jesus (a) when he ascends to sky to be Elijah (a).