I read them using Good Reader on my iPhone with no problems.

I kind of like the concept of allowing for a difference between doing something cautiously and recklessly. It seems to me that the difference in result range between Fudge dice and d6-d6 nicely represents this if you allow players to choose for each action which they will roll. Am I missing any implications that would make allowing this ill-advised?

Another point, though this might be minor: How will you have him revert to his normal side after he's gone Dark? I doubt the character himself would willingly seal his persona, and no one on the team will probably know about the dark side much less how to seal/release it, right?

Actually, now that I think about it, you could just give the dark side a time limit. Or have him go dark only under specific (and temporary) circumstances.

Or compel a different aspect to 'break him out of it'.  To  borrow an example from a different universe, Xander gets Willow to come down from her 'Dark Willow' rampage in season six of Buffy by compelling her Friends Forever with Xander aspect (Yeah, I know lousy name for the Aspect, work with me here).