I'm too lazy to type it all up again but here is the Reddit thread where I answer most of the questions you'll have, as well as pictures of the box.
http://www.reddit.com/r/boardgames/comments/1byp4q/custom_sentinels_of_the_multiverse_storage/
Dude, that's awesome.
That's the same box I use. Adding the felt is an awesome idea.
I sleeve all my cards with FFG sleeves and I use extra decks for all the promo alternate heroes and villains so that means that right now the box is maxed out with no room for tokens even, which will be an issue for future expansions. I think when vengeance comes out I'll have to store the cards vertically, which should help at least fit that expansion... after that, who knows. I'll have to come up with some other solution.