Just remembered i was gonna give you a run down on a few of the issues i found with my 09.
Some of the obvious things are the bottom chain roller doesn't line up with the chain properly and needs a cut and reweld to correct.
The rear brake line rubs on the swingarm and would eat away at the alloy if left ( i stuck a piece of rubber on to fix it see pic )
The airbox design is a disaster and required me to radius the carb venturi to fix it, from stock there is a horrible square edged step because there's no relief in the air boot. While i was in there i tidied up the carb to rubber sleeve and sleeve to reed junction as it was out a little. This isn't just a TM problem though, my CR was worse and the TM barrel to cases had already been done by hand in the factory.
The fuel tank rubs on the frame quite badly and needs some rubber strips for packing too.
Not much really but i think the airboot issue robs a little power and needs fixed. Would be interested to know if the 2012's are the same.
Here's a look through after i tidied it up you can see how much i radiused the venturi
Heres a look into the airbox after in radiused it too, sorry i havent got a before pic but you can see how much of a step there would've been.
I just cut a piece of inner tube to shape and glued it, hasn't moved since.
I re routed the wiring loom too as i wasn't happy with it stock, looks much cleaner there. also after thios pic i turned the coil around so the ht lead wasn't as visible, much tidier.
The exhaust outlet had this little indent in it, apparently it's common. little epoxy fixed that.
I was never happy with how the kickstarter sat and after i tweaked the pipe the kicker rubbed on it. I swapped it for a late model CR kicker, problem solved.
The most recent pic, i've put a hammerhead shifter on since then though.
Hope some of that helps, I also highly recommend you check to make sure you've got the required pressure in your fork bladders, mine didn't from new. Without that 5 to 6mm of convexivity those marzocchi's are pigs. don't over inflate either though as the slider still has to be able to clear the bladder at full compression.