The interference at the clutch cable can be dealt with by using a WR clutch cable. The boss to mount it up to should be on the top of your crankcases. Or, as you have noted already, you can cut the case off. On the YZ's the ignition covers were magnesium in some cases, so check before welding. Using the WR crank, there should be no problem using the flywheel/stator, and no spacers should be required. A WR can be modded in several ways. Leo Vince and Vortex both make ignition boxes for them, and a set of YZ cams and some carb tuning will basically turn it into a YZ engine. Then, you'll have the fat 5th gear, and a lower 1st for the tight spots. The forks can be swapped with '06-7 YZ forks ('08 would need a different caliper and front axle), or they can be reworked very successfully. How much you should spend. That's hard to say?