I would seriously look into a 4mm Serval or Driveline motor.
Alloy Bolts has bolt kits for the entire bike.
Replacing all clutch parts at the same time is highly recommended.
Yes, you'll have to split cases unless it's something on the clutch side.
You can pull the stator/plate and the clutch parts and flip the motor over.
No need to pull the top end.
That’s just a vent hose. I just run it forward and down and zip tie to the frame. Do not run that to the carbs. If you have coolant in your oil, your water pump seal is bad.
Alloy Boltz is a BansheeHQ sponsor. They have stainless bolt kits. Here's a link to all their Banshee stuff.
https://alloyboltz.com/product-category/import-motorcycle-kits/honda-import-bikes/yamaha-yfz350-banshee/