Take a video of it, upload a link most all phones these days take HD video with great audio, heck my i phone 4 takes better video than my $500 sony handycam!
My friends 06 also knocked, normally the loudest just after startup when cruseing down the driveway at 1/4 throttle. His sounded like the wrist pin was very loose or maybe pistion slap. and it would come and go depending on throttle, We just ignored it and kept the oil clean and full= no problems yet!
******** edit, just seen that there was a second page to this- yup a decomp system sticking sure would cause that noise, I will tell my friend! Did you find Any metal pieces that would harm the engine??

 

No metal fragments found.
I'm waiting on a new cam and talked to a mechanic over the weekend. He said the knock is actually from the piston slap and is a side effect of the defective decompression cam. As I understand it the engine warms up the rings and piston expands and goes away. The piston was in great shape but continued use of the ATV with a defective decompresser cam will eventually cause classic wear of the piston skirt and cylinder. There are two exhaust valves and the decomposers opens up one longer than the other. This imbalance in the compression causes the piston to compress unevenly and causes the knock. A working decompressed cam is meant for easier starting and goes to normal valve opening once started.
Pretty much it. If I'm wrong I'll be back here.

 

Did the cylinder and piston measure out ok with a micrometer?

 

Yes it was with in specs.

 

Yes it was the decompression cam causing the upper end engine knock. I'm still puzzled what actually causes the knock - Piston slap, (which there is no sign of), or the sound of the compression release on the compression stroke do to a stuck open compression cam mechanism.

Whatever - it worked and better power as a result.

Safe riding.

Dennis

 

Those decompression things are known to make a knock noise when bad, though I'm also not exactly sure how. Maybe valve acceleration is way too steep at anything above idle...

Anyway glad you got it fixed.