The current story arc in Mighty Avengers has the team forming and immediately having to go out and deal with a Mole Man incident. As they first respond to the Mole Man monster, they mention the fact that they hadn't even had time for a training mission before going on active duty. That threat directly morphs into the Ultron story with no rests in-between.

However, in New Avengers, the underground team has been pursued by the Mighty Avengers. I assumed that those NA issues simply took place after the initial Mighty Avengers arc. But in the most recent issue of New Avengers, they are affected by an EMP generated by Ultron, meaning that the current NA story takes place simultaneously with the Ultron story.

So there is no time for the Mighty Avengers to fight the New Avengers after they've formed but before they face Ultron.

That's a real mess. This isn't geeky "Why doesn't Banana Man remember that he can defeat the Flaming Artichoke by funneling mustard gas through his loin cloth, like he did in Tales of Anticipation #13?" continuity. This is very basic "where are your characters" continuity that any writer of fiction needs to keep track of. And if Bendis (who i love), the writer of both books, slips up, why doesn't his editor Tom Brevoort (who i also love) catch something like that?

Hopefully this will be resolved somehow. Is there time in the Mighty Avengers story where they can go after the New Avengers that i missed somehow (the issues are currently in the borrowing chain)? Does Ultron release a second EMP in a future issue of MA? Were the Mighty Avengers in the New Avengers story actually Skrulls?

If there is no answer, i'm gonna have a hard time placing these comics in my collection.

I'm also curious how this all fits in with World War Hulk.

But, was the whole Mighty team in those New Avengers issues. If not, perhaps this was an 'unofficial' the team's not fully formed type of mission.

I agree. It makes no sense, I just figured they were two separate "comic book world" storylines until I read the last one. I figure maybe it could've happened before Ultron came and took over, but it doesn't really work out.