I am not an expert or anything, but wouldn't you need a spring-loaded type of assembly? If you put a larger wheel on their, it would grip until it wears down and leaves you with a shuffling problem again. Also, you are changing the way the train moves through the circuit by adding more friction, which could slow the train down.
Last summer I built a 35 or so foot long rollercoaster in my backyard. No upstop wheels but the guide wheels I noticed the closer they were to the guide rails, it would slow down a little bit, but it went even slower when it shuffled back and forth when I didn't have the guide wheels installed.
No, it would not likely work, because the reason why there is a gap between the wheels and the track is because Vekoma and Arrow intentionally designed some turns to be tight. This means that actually, at some points in the ride, both guide wheels are infact touching the rails. These mainly occur in the unbanked turns that are taken at low speed.
So in essence, the car would get stuck in the turn if the wheels were bigger.
I spoke with a certain wood coaster engineer that said a lot of the roughness of wood coasters comes from the way the track is supported. As he put it, the track itself is like a "noodle" that gets less rigid over time. Eventually it starts to "washboard" between supports, which taken at high speed accounts for a lot of the roughness. Better support strategies keep the track better supported and help prolong the life of the track.
You can't just have all of the wheels firmly grabbing the track, as the cars wouldn't be able to negotiate anything other than a perfectly straight piece of track. As a result, coaster manufacturers are forced to allow for some room between the wheels and track in order for the vehicles to go through whatever crazy inversions and turns they have in mind. However, you're correct--this "gap" also results in unnecessary banging around. (Keep in mind that the transitions between elements also plays a huge part in head banging, which is why older Arrows are always rougher than a B&M with "rough wheels", so to speak.) B&M, Intamin, and most recently Vekoma (and possibly Arrow?) have fixed the wheel gap problem by installing spring-loaded wheel assemblies, which keep the train from bouncing around while still giving the wheel assemblies necessary room to move. If it was as easy as installing larger wheels, Arrow and Vekoma would have done it ages ago--those people aren't idiots, after all.
There is typically a gap between the track and the guide wheel in order to give the axle room to swing, also to accommodate the fact that the curve isn't exactly tangent to the axle. The typical Arrow-type wheel assembly will cruise straight between the rails until the leading guide wheel on the outboard side of the curve hits the rail. The axle rotates until both guide wheels on the outboard side are following the curve, at which time the car starts to go around the turn.
I haven't investigated fully, but I suspect that at least one item of note is the distance between the guide wheels. I say that because of the difference between Iron Dragon and Top Gun, since Iron Dragon shuffles like crazy and Top Gun does not...the big difference that I can see is that Top Gun has 12" guide wheels instead of 8" wheels, and out of necessity the axles must be further apart. Wood coasters, of course, don't have dual guide wheels, but they also don't have steerable axles. Instead, the whole car has to steer around the curve, as the whole car operates much like the Arrow axle. The problem with that is that the car has to slide on the rail because the road wheels don't steer. That's why the tracks have to be greased or graphited on most wood coasters.
What complicates things even more is that the train is steering multiple cars on a track, and because the cars are tied together, what each car is doing affects what all the other cars are doing. I suspect that's what is causing a lot of the shuffling on Son of Beast.
Vekoma should have switched over to the Invertigo trains a long time ago. That would've have solved all the SLC problems, as they have B&M-like wheel assemblies. If you go and ride Mind Eraser and then Two Face at SFA, you'll notice a HUGE difference in re-rideability.