Can Fortress Maximus have a different head than Cerebros?

No. Fortress Maximus is just like other character cards with a body, except it's bigger, and it must have Cerebros as its head. Cerebros is unique in that it has both a head mode and a body mode. So it starts the game attached to Fortress Maximus, but you also get another head to put onto Cerebros. This can be Emissary or any other character with a head mode. The stars from all three cards count toward the 25-star limit. Note that Fortress Maximus, Cerebros, and Emissary have 25 stars combined.

Does Fortress Maximus get the bonus from Cerebros' Head?

While Fortress Maximus is on the battlefield, it gets the Bold 1, Tough 1 bonus from Cerebros, but it doesn't get the bonus from the other head attached to Cerebros. That head's bonus will apply to Cerebros after it's deployed.

What do you do when Fortress Maximus is KO'd?

If Fortress Maximus is KO'd, you put Cerebros back onto the battlefield in body mode, with its head still attached. Because a character can't flip into head mode, Cerebros won't be able to flip while it's on the battlefield. If Cerebros is KO'd, you put its head onto the battlefield in bot mode.

Can I play Emissary with any character that has a body mode?

Yes. Emissary is just like other character cards that have a head mode and a bot mode.

With Fort Max, the second Head counts towards the TEAM star total. Does it also count towards Fort Max's CHARACTER star count or is that just Max and Cerebros stars combined?

While Fortress Maximus is in play, he and Cerebros's stars make up the character's star count. The second Head is not counted.

On my starting team one of my characters is Quake with a Flintlock. Can I sideboard in Fortress Maximus if I also put Flintlock on him?

You can't play Fortress Maximus without also playing Cerebros, and vice versa. Since you can't put both in your sideboard because you're only allowed one character in your sideboard, you can't sideboard Fortress Maximus in any effective capacity.