I don’t know the diameter difference between the stock 350 and R1, but, if you have the ability to machine things, you could probably ream the stock hub bearing seats to accommodate the R1 axle. Probably. That would require the fabrication of a new retainer, rotor adapter plates, and some axle spacers. All very achievable if you have equipment, skills, and time.
The Cognito hub is by far a more elegant solution and is already solved. Plug and play, if you will. You should also know that using their hub (and perhaps if you modify the stock hub) they use an inside-inside spoke lacing pattern to keep the spokes away from the calipers and still reach the rim. It requires a different spoke length than stock, so custom spokes for stock or Cognito are required for an R1 conversion to a laced wheel.
Swapping in the front end, you are changing the fork offset from stock steering geometry. Something to keep into consideration. You are bringing the forks closer to the engine, so be aware of potential conflicts to the exhaust (not normally an issue on the 350 with a USD conversion).
As for “Scramblers” in general, they re not well suited as 4 cylinders. Almost every one I can think of that was factory made are twins or singles. The added weight, width and mass don’t lend themselves well to the function of Xroad riding. But I get the aesthetic appeal you’re considering. Since it likely won’t be a Xroad rider in fact, you can abandon some of the constraints and resolve the high pipe routing for a 4:2. That will be enough of a challenge.
Anxious to see what you come up with