If you want a 5.0 rear rim the stock hubs fit fine and they aren't very expensive.
The front there is no reason tho put on KTM stuff unless you just want to make your life miserable searching for spacers relocation brackets and parts.
For the rear just make a longer spacer on the sprocket side, the same thickness as the sprocket, or a washer if you want to wrestle putting it in and a spare sprocket under the rear sprocket. A 1mm shim under the countershaft works fine in the front. If you don't need your MX wheels this is the way to go then you only need your spokes and rims.
It seems foolish to put KTM stuff on there the axle isn't even the same size, sounds like a lot of problems to me. Not to mention Yamaha hubs are inexpensive.
If you want a 5.5 rear wheel to stock hub then you will have to widen the swing arm 10mm. and go 8mm wider on the axle and sprocket spacers. A propane soldering torch and bottle jack are needed too.