I've heard the gears are more narrow, but have never heard of any problems like gear failure etc. They are definatley taller, I can tell you that.
An aftermarket frame is the way to go! Much less motor mount cracking, You dont have to make the mounts, they're lighter, and an aftermarket frame will always handle better. But you don't race so it's probably not a big deal.
My problems are exhaust and intake right now, the usual.
2009 CRF250R
R.I.P. Kelly "Steelrod" Chang, Todd Vescovi, Matt Barosek, & Jeremy Lusk, You'll Never be Forgotten!