Sorry to hear that, seems to be the theme of the FI world, at least for us 2010-11 guys. While mine isn't tune related I've been down for two weeks with a broken tensioner. Getting a new piece machined here on Friday. Hope you're up an running soon.
I'm sure the issue is in the tune. But a bad MAF sensor may cause the misfire. I've had more than my fair share of busted MAF's.