First on the docket, who do you think Hohenheim transmuted? In the flashback at the beginning of 45 you see him start the alchemic reaction with a clap. This means that one of the sins is 400 or more years old; as we know Hohenheim was still in his original body. That leaves us three choices, Pride, Envy, and Gluttony. I am more then extremely doubtful it was Gluttony, so now where down to two, and they’re both extremely hard to pick from. Pride would fit as if he’s the leader you would assume he’s also the oldest, but then again Envy hates Hohenheim specifically. This was seen when he was literally kicking the crap out of Ed in the Fifth Lab because of his relationship to him.
This leads me to my second stream of thought. In the same scene where Envy mentioned him refering to Hohenheim, he also mentioned him as a leader. Now maybe it was just the fan-subs, but don’t all the sins repeatedly refer to their higher up as "he", including Pride. I was under the impression that Hohenheim would be whom they where referring too, but seeing as how both Gluttony and Lust had no clue who the hell he was and if what I’m assuming happened to him in the basement happend I think that rules him out. Do you think perhaps there is someone else, or they where referring to Dante as him on purpose?
Is anyone else unnerved by the amount of time Roy was alone with the Furher/Pride? Think it’s possible it wasn’t Roy who walked back out? That’s just a passing/closing thought though.
Finally I'll close by daying that Winry's Doctor father is not dead, he's just gone back to the future.