See if you can wiggle the countershaft (front sprocket) front to back. This may cause the chain to be misaligned with the rear sprocket no matter what the rear marks show. The only fix for this is to replace the bearing behind the countershaft (splitting cases). This would be
VERY rare and more than likely would be caused by improper chain tension (too tight). If you are using an o-ring chain, you may need to purchase a front sprocket spacer to compensate for the increased width of the chain. Check out
Fastway for this spacer. Also make sure you are adjusting you chain properly. The bike should be off the ground with the swingarm fully extended. Check you chainslack at the end of the swingarm chainguide/protector. I think on the CRF450R it should be around 1 1/4" or 32mm (Honda says 1 1/5 or 30mm which would be just under 1 1/4", but the 1/4 is easier to read). When you are done adjusting your chain, the rear wheel should freewheel with an oiled chain. You might even spread the rear caliper apart to take its friction out of the equation. When you are tightening the axle nut, make sure to push wrech foward against the adjuster and not pull the wrench back or up as this will pull one side back some.