I just checked out that USF vs. Navy game and saw some pretty gaudy stats. Navy had 299 yards passing and 317 yards rushing? Holy offensive balance, Batman! It's crazy you guys won that game and barely edged them out at 626 total yards of offense. I might have to watch that game sometime.
With that out of the way, I don't think Charlie Strong or your DC have any experience with stopping the flexbone and that may be your downfall. We are 10-0 in the last 10 seasons against rotating ACC Atlantic opponents because of the advantage its uniqueness gives us. Paul Johnson has seen pretty much every defensive front you can give him, but your team hasn't seen what our offense can bring. It's just an experience mismatch. What generally knocks us down offensively when we face uncommon opponent is when they have an elite linebacker (2012 and 2013 BYU's Kyle Van Noy and 2015 Notre Dame's Jaylon Smith). If you got one of those guys stored away, it could be ugly for us (especially with rain).
I think your best bet is to try to win in a shootout. Ordinarily I'd say you'd have no problem putting points up against us, but I'm feeling weirdly optimistic about our defense with what Nate Woody put together on Saturday. Echoing what you said though, performance against an FCS team is really difficult to gauge. If your kicking is anywhere around average, you could possibly beat us just by matching our touchdown total and making your extra points.
For the last question, turnovers are always going to be a concern. First one was a bad fumble, second was a weird overthrown ball where the receiver fell (got pushed?) down, and the third was the backup QB pitching to a third string RB who bobbled the ball. The first one is inexcusable, but I am willing to give a pass on the other two as first game jitters. Overall, I think our strengths just match up a little too well to your weaknesses. But we'll see on Saturday!