There's got to be something we're missing here. I've seen some people strip their gears 3 times in 10 minutes, and I've seen people run a season with no issues. It didn't matter if they used the new 2 speed clutch or the new material gears. Some ran 4mm chassis, some 3mm. Some had some brand of aluminum brace over the motor, some still had the stock plastic piece. Some had a blade swaybar, some had the the wire. Not sure if it's specific to one particular motor or not (although I know some RBs have interesting fitment issues).
The only thing I know for sure from running the Mugen this year is I've only stripped a gear if the motor wasn't meshed right and my bulkhead screws weren't tight. This was running either the 3mm or 4mm chassis. I set my clutch on my Ninja with the thrust bearing spacer (the best way to get that gap right) and ran the thigh wire swaybar. As long as I took time to set the mesh right (I pulled the 1st gear spur off and set the angel and mesh with 2nd gear) and did a quick check on the bulkhead screws, I had no problems. This worked with the old gears and the old 2 speed. I've since changed the 2 speed when I replaced some of the drivetrain parts, but I'm not convinced that made any difference.