With the hex couplers it appears you are using, it’s really easy to install them such that the resulting hex “shaft” is not perfectly straight. At 6000 rpm, anything other than an axially straight shaft will cause substantial vibration. Also, the Colson wheels are likely not to be perfectly dynamically balanced. Again, at 6000 rpm, slight imbalances will cause vibration.
I’d recommend that you try a redesign to belt drive a straight Thunderhex shaft in round Thunderhex bearings. It looks like you have CNC capability so it should be pretty easy to design and cut some new side plates. See how much that change reduces your vibration. I expect it would be a lot.
If there is still some or even a lot of vibration, you might try rotating one Colson wheel relative to the other to see if a different alignment improves dynamic balance and reduces vibration. If you have more wheels, you could also try different wheels along with different relative alignments. I’ve heard of people using a go-kart wheel balancer to dynamically balance shooter wheels, but I have no experience with that. If you have any connections with a local racing scene, you might be able to get good dynamic balance with less trial-and-error.
One more suggestion that you didn’t ask for…it might seem like having the gap between the Colsons could help the Power Cell track straighter through the shooter, but it likely would want to move to one side or the other like a wide belt would if you put it on a roller with two crowns. If you have the capability, you may want to turn down the hub on the inside of each wheel so they are very close to seamlessly touching. You might also want to turn down the slight crowns on both wheels so the surfaces are perfectly flat. You might improve your shooting accuracy with those modifications. Of course, if your accuracy is just fine as-is, there would be no need to fix what is not broken.