Make sure the pison is on top dead centre(look through the small timing plug hole down the bottom) There is a punch mark on each cam sprocket that aligns with the cylnder head surface. the cam lobes facing away from the lifters
Im trying to up load an image of the page in the manual
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May 01, 2010- 
hope this opens for you
SOURCE: timing on 06 yamaha yfz 450
Here is the SERVICE MANUAL for your bike.
http://pdfdatabase.com/download_file_i.php?file=14074911&desc=Yamaha+YZ450F+Service+Manual+.pdf
SOURCE: carburetor adjustments yamaha 450yfz 2004
Turn both the air screw and throttle screw inward until they LIGHTLY seat. Now back each one outward one and one half turns. This is the factory setting. I am going to give you a web site where you can download a free PDF factory service manual for a YZ450FR. I believe the model is a bit different but the carbs are the same.
Go to this site and you can download a free PDF service manual. The site may take up to 25 seconds to fully load the list of manuals. It is worth the wait. www.carlsalter.com/motorcycle-manuals.asp The service procedures are there in detail and a lot of diagrams and photos. Don't mess with the pilot screw unless you have to, Part #11 in the diagram.
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SOURCE: Yamaha YFZ 450 engine serial number
im unsure but arent they on the sterering stem on a metal stamp or perhaps under the gear shifter I am unsure
SOURCE: how do you set the timing chain on a 2006 yamaha
1st set piston at top dead center, which is the top of its travel. after you have verified top dead center, and you are 100% sure its at top dead, install the cams. first the exhaust cam, with you facing the sprockets, with the cam lobes facing up and away, about the 10 o clock position. once set there, you should see a refrence on the sprocket, with lines that will be parallel with the cyl. head surface. then install the intake cam, with lobes facing in the 2 o clock position. once again, you will see refrence marks on the cam sprocket that should be level with the cyl. head surface. after the cam caps are installed, and the cam chain tensioner, turn the engine with the flywheel bolt to verify you have no piston valve contact. after you turn over a few times, recheck timing.
SOURCE: how do i change the oil on a 2008 yamaha yfz 450
Remove sump plug on slightly warmed motor (Not Hot!) keep bike straight up once emptied replace sump plug and refill 1 litre of oil
would highly recommend you change the oil filter as well though ?
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Are you referring to where the timing marks on the cams should be at TDC?
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