No need to strip the motor, Yamaha supply a special replacement seal without a lip on the end.
I changed one on my sons fazer 400 about 3 years ago.
Taking off the rotor was my biggest problem I had to heat and it came off eventually with a such a noise that I thought I had broken the crank.
The special seal part number is 93101-29166 and it is about £25, which is over twice the price of the standard seal.
You will need a special sealer, I used RTV 1080 Silicone Rubber Adhesive Sealant.
Carefully drill a small hole in the outer section of the seal sbout 5 mm deep and prise it out with a small screwdriver working bottom to top. It will collapse with supprising ease. Take GREAT care not to scratch the surface of the crank. When the seal is out clean the area with something like thinners, which evaporates without leaving any residue, let it dry well and apply engine oil to the seal lip and the sealant sparingly to the out part of the seal and push it home.