I was removing the cylinder head cover, and right as i was lifting it up, a keeper dowel fell down into the cam-chain area never to be seen again. Tried looking around with a flashlight and a small magnet. no luck. any ideas where it went?

You will not like my suggestion.  The best thing to do is remove the right side cover.  Leave it off until you get the top end put back togeather.

My suggestion is to remove the right side cover also. I had to do this recently and it is not difficult. It will assure that you find the missing dowel.

Now you have a good reason to change out your cam chain as well...

And you might as well clean the bottom oil screen whilst you are at it. Check out my last topic if you want to learn from my mistakes re removing right engine cover.

Took the right side case off. fished around with a flashlight and a magnet for what seemed like hours. I even used a borescope to look around with no success. Right as i was giving up I looked down and saw the reflection of my flashlight on the dowel. It turns out that when you drop one of those dowels down the cam chain area, they sit right below the cam-chain on a little ledge. It looks like you could possibly get it our without removing the cover if you had a magnet that was small enough to get around and under the cam chain from above. I used a magnetic tip screwdriver to get it out. Case solved! When it initially fell I thought i heard more clinking like it fell deep inside the motor, so I was surprised to see it in this spot.

I did clean the little screen while I was at it. Why would I need to change my cam chain? Is there an issue with them? Mine seems to be in great shape and the motor shouldn't have that many hours. I am only topping the bike because it had some sand get past the air filter after my uncle borrowed and incorrectly installed the air flilter.