2005 R6 Cam Timing Help?

U do nothing wrong, just keep going.

And the Manual doesn't say "perfectly"

You might have a slight amount of chain stretch, but not enough that I would have any concern about.

But to be honest, from your photos: Your trigger wheel looks like it isn’t lined up exactly at the crankcase seam and the EX cam line is slightly higher than the head. It looks to me that if you rotate the crank just a hair more so it lines up with the case split, the cams will be perfectly aligned. I’d bet you are right on the money.

Chain stretch makes sense.
I really hope the stretch isn't too bad. I'm not really up for changing the chain and sprockets right now.
The camera angle is a little off, but the rotor T mark is much better aligned in reality.

Oh btw, if I replace all chain guides, will that fix that slight misalignment?

Looks right in the money to me

Following up.... finished the job after 4 weekends.
I still hear the chain rattle. Rode without helmet today for test ride, so not sure how loud it was in the past. But the bike feels alive! I changed both fuel pump & filter besides valve shim job. Even with 0/-1 sprockets, I was able to wheelie in 2nd gear. Never was able to do that in the past! Whether it’s the new fuel pump, or the valve job.

Thanks guys!