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05 RMZ450 bottom end rebuild. HELP!?

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Well, bottom end is where I need help, anyway. Grenaded RMZ450. Dropped a valve which smashed up the head, piston, and bent the crank.

Been very meticulous and careful throughout assembly. Everything is spotless clean and, I'm 99% sure arranged and installed properly. This isn't the first motorcycle engine I've rebuilt, but it's the first single cylinder like this.

Anyway, the problem is, the transmission. I cannot for the life of me figure out what is wrong. I've split the case and tried 4 or 5 times now, and still no luck. The transmission seems to spin and shift through all the gears properly when I've got it assembled in the left half of the case. But once I have the other half of the case on and start tightening it down, the countershaft binds up and stops spinning. The driveshaft still spins freely, as does the crankshaft. Can anyone help me out here? I'm completely lost. All the gears, and shims, shift forks, etc. are in good shape and in their proper position as far as I can tell from the manual. I can't find a lot of info searching various forums. I'll be hugely in debt to anyone who can help me get this sorted!

(Oh, and since I see some people interchange the names, by "coutershaft" I mean the one between the crank and the driveshaft. By "driveshaft" I mean the one that holds the front sprocket for the drive chain.)

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I'm just about to redo an 07RMZ450, from the "bottom up"  Got the motor in 5-boxes.  I can try to help, heck mabee we will end up helping each other.  Did you fix it yet?  The counter shaft has fixed gears on it.  Ie all are tied to the shaft via splines.  If you are in neutral I can see how the drive shaft spins, but not the counter shaft, if you have put on the primary drive gear, how can the crank rotate if the counter shaft is binding?  Do you have a washer out of place and the shaft is binding agains the case?  Is the case closing properly?

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