I use a 14 ft aluminum with a 25 jet drive. The North and South Forks are pretty small rivers, but there is some decent current at times, but I've only kayaked around there before. Mostly I spend time on the Potomac and Monocacy rivers with my jet boat.
You're probably not gonna want to be on a plane in 3 inches of water on any river, unless you've got one of those 100k battle armor jet boats with the tunnel hulls. You'll hit a rock for sure, and it will destroy your boat or worse. The only time I'm running on a plane is when I know the water is deep and I've been there before. If you hit a rock with a bass tracker in a river at planing speed, that thing is toast.
So the boat with the 48hp jet drive sounds like your best bet for what you want to do, hands down. You'll have more then enough power. I had my 250 buddy on mine at Deep Creek Lake this fall and we had no trouble speeding around the lake at 25 or so mph on plane, in wind. At 16 ft, that boat would be small and light enough to drag over gravel bars - and believe me you will need to on those rivers and most around the area, especially in the Summer months. You'll also need to be prepared to be able to raise the drive from time to time to clear rocks and gravel from the drive intake grate. A 48hp motor is pretty heavy. My 25 is heavy, and I wound up with a sports hernia that I'm still slowly recovering from(hopefully avoiding surgery) when I had to pull that thing up from inside the boat. I'm going to build a pulley system this year, you might consider the same. Those jet drives usually get clogged at the absolute worst times, like when you're going up a shallow gravel bar with a ton of current, and start sucking up crap, then you have no power and you're drifting back down the river.