I'm not sure if Brushy Creek Lodge still does shuttles, I've never used the service myself. I'd give them a call.
As for the terrain. From Hwy N to Hwy A will be the toughest, hilliest section. The hills aren't too bad though, the highest point in the state is only 1,772 ft. There are also a bunch of glades on that stretch that can turn you around but just watch where you're going and you'll be fine. After you pass Hwy A the trail mostly stays in the woods. The Middle Fork section is one of the newer sections and is really nice. The worst places I can think of for water crossings will be Ottery Creek at Hwy A and Neal's Creek. There is a bypass around Neal's Creek but I've crossed Ottery Creek when it was over knee deep and it was flowing pretty hard. Other than that, most of our creeks are pretty mild affairs.
I think you've picked a good trip, you'll get to see both sides of the Ozark Trail; the old, rugged part and the newer stuff. I'd suggest the side trip to Bell Mt if you hadn't planned on doing it. Its a few miles out of the way but is a great place to eat lunch or take a break.