Whenever I want to see what’s the same and what’s different between the two bikes, I start by looking up the Yamaha part numbers for a particular part on each bike. I've found that many parts for these two bikes share the SAME part number and some of course are unique to the WR or YZ. For instance, the cylinder part number for an '01 YZ426 is Y5JG-11311-00-00, and for an '01 WR426 is also Y5JG-11311-00-00... same cylinder, same part number. However, the rear fender for the YZ is Y5BE-21611-00-00, and the WR is Y5BF-21611-00-00.... different fender, different part number. Now, I'm not certain its an absolute rule that the same part number = same part, and a different part number = different part, but it would be logical to assume so and I've personally found this to be the case. Seems like Yamaha tries to use the same parts between the two whenever they can, which would make sense from a business perspective as different parts means different tooling to make them, a larger spares inventory, etc..
Anyway, back to the trannys,, I went out to PARTSFISH.COM and took a quick peek at the parts diagrams for the '01 YZ and '01 WR trannys, and it looks all the gears and many other parts do have unique YZ or WR part numbers. Seems strange, cuz I thought I remembered reading something about it being just 2 or 3 of the gear ratios being different between the two bikes,, not all of them. I suppose the two bikes could indeed share some common gear ratios, and use different gears to do it (a 1:2 ratio same as 5:10, but 1 isn't 5 and 2 isn't 10).
What do you think Rich, have you dug through these trannys any??
By the way, when I had a YZ and wanted the WR gearing, I also thought about trying to change trine gearing, but I wimped out and sold the YZ, bought a WR,, and "ZYed" the WR (seat, tank, plastics, suspension, etc..)