I wonder if if what you all are describing is actually buffeting. Buffeting is NOT the act of repeatedly gorging yourself at the all-you-can-eat seafood buffet in the casino.
buffeting [noun] (pronounced buf-fet-ing) is an "irregular oscillation, caused by turbulence"
buffet [verb] (buf-fet, NOT buf-fay

) is to "strike repeatedly and violently; batter (especially of wind or waves) "
Travelling at up to 95 mph in an open air train will do that to you.
I ride motorcycles and the battle against buffeting is a constant battle for riders who ride long tours. Motorcyclists are always talking about different windshields (and buying new ones, and modifying sizes and shapes) and helmets to minimize buffeting. Fury has loads of buffeting, some seats have more than others (the turbulence varies at different speeds and different locations on the train). That's just the nature of going that fast in the open air, in an incredibly un-aerodynamic vehicle, very similar to riding motorcycles at high speeds. And depending on wind direction and speed, the buffeting gets substantially increased or decreased.
Although the thunking mentioned above, going up the hill, definitely sounds like bad wheel or bearing. And that can certainly be fixed easily.
The only way to stop buffeting, would be to suck all the air out of the area (bad idea for breathing) or to enclose the people inside of a sealed and aerodynamic train (which would be no fun).
I find row 3 to be the row that I notice the least amount of buffeting. I would also say the ride has always been very smooth. The only roughness I have noticed is the buffeting (which increases and decreases depending on seat, and wind). Stick your face out the windows of your car as you go 70+ mph down the highway (no, don't really do this). You'll have a headache in a couple minutes. Again, that's the nature of traveling fast through open air.