It sounds like you have the hard part figured out A1, the story. The rest is all your personal choice. While I don't believe you can give a temp power reward, the rest is all user selected, and you can make it as challenging as you want. Mine had 6 arch-villains... it was a *ROUGH* mission that needed a bit of toning down before it was humanly possible. But we persevered and managed to get through it, and boy did we earn our stripes doing it!
The only real difficulty tip I can give is this : Make sure you vary your minions and lieutenants (create a few versions of each) so that you don't end up with like 10 stacked debuffs of the same type.
You can try making it more than one mission, but I found that when you're using custom enemy groups, one mission is about 60-70% of the "space" they allow you to use for your mission, so I cut mine into two seperate "chapters" which were individual missions rather than an arc.