On a general note, the whole thing is still beta, as the name says, and a few things aren't implemented yet, so keep that in mind. I also can't get too specific, obviously, but I'll try to answer you as best I can.
Does it seem like it will take a lot of work to port over an existing game to the FAE version? We have 5 years of campaign history and I am hoping it won't be a headache to translate all those characters.
Well, as with all transitions between games, I would probably do them by creating the character new in the other system the way the character is now. That should work well here, as quick and easy as that works, especially since you've got the aspects already, which can often take quite a while when coming up with new Fate characters. You'll probably be done in a few minutes. There are aspects of grown characters that might not translate to the system as it is now, but solving exactly that issue is put up under "to do".
Looking at the characters in the games I run, I don't think I'd need to stretch things too far to convert them satisfactorily right now.
How customize-able are the characters?
One thing that's always put me off FAE is that the characters feel same-y to me, I'm hoping the Dresden Files variant manages to avoid that.
Well, we're talking FAE, so we've got the 6 approaches, and there's only so much variance in that. If that's what has you worried, there's not really a way around it, I suppose.
In our test game, we've created a medic, a pixie and two wizards. Despite the wizards only differing in one stunt, they already feel very different. However, they draw a lot of that difference from their descriptions and their aspects, not so much the mechanical side. The pixie and one wizard have exactly the same approaches, when it comes to numbers, but will use them vastly different, so that should work out as well. So far, nothing about any of the characters feels same-y, not the same character types like the wizards, but definitely not the different ones, there's a lot to make them very unique. I'll see if that changes once we get into the action, but I doubt that.
The option to create your own stunts/powers is still there, as well, which should give you plenty more opportunities to customize, if need be.