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Yes the 06+ have a weak tranny but 04-05 have a crappy crank! So yall could have your share of problems
the 04/05 crank issue was with the original cranks. Honda came out with the updated crank in late 2005 and the old crank was discontinued. so all of the 04/05s that had the crank go had it replaced with the updated crank or hotrods crank which is "updated".

how often do you hear of 04/05s having crank failures now a days? its a rare thing now. in fact 06+ have crank failures more often now a days. but its a race motor so parts do eventually wear out.

if a crank goes out that has 1,000 hours on it... that's just wear and tear... nothing on a race motor lasts forever. even the bullet proof 400ex can have crank failures but what you never hear about now is how many hours it had on it or what kind of abuse it went through.
 
pros of the 06+ motor
better carb and piston stock so more power out of the box
more potent HRC kit

pros of the 04/05 motor
carb and piston can easily be changed so boo ya 06+
stronger tranny and better gearing for the race track
stronger cylinder and skirt design which can handle a lot more stress than the 06+
hands down better once race built
 
I had 04/05 bikes and 06, i like the motor on the 04/05. And some say they have crank problems but that's he old cranks even the 06+ I have bought that the crank failed! I bought a really low hour quad, super clean I mean really clean! It had shot crank!
 
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