You need to set the video to "public" so we can see it. Offhand, at 3K unless the bike has been REALLY thrashed and run out of oil or something it would be tough to imagine the chain being that far out already.

This is cam chain noise.
https://www.youtube.com/watch?v=txBAxgXLlwc

Get a mechanic's stethoscope or a metal rod, a wood dowel about a foot long, or even a long screwdriver and put one end of it on different places on the engine and press the other end inside your ear, you can REALLY hear engine noises better. Two places to check are on the clutch side just to the right of where the clutch cable goes in, that's where you'll hear chain noise. Then the upper part of the engine where the valve covers are, front and back. You'll be able to hear clicking valves. The Savages are noisy beasts to begin with. Some folks say if you use 15-40 oil it quiets them down some. I'm going to try that at my next oil change.

It sounds like my bike that has 3000 miles on it too. I don't hear anything unusual, definitely nothing like the cam chain vid I posted. If you did the stethoscope thing on the top end you'd definitely hear the valves clicking if they are loose. You might have been getting some blow-by on the header gasket if it was loose. That'll make noise too. I'd say ride!  

The header bolts to the cylinder head....should just be snugged up with a 1/4" drive ratchet.....and only one hand. They should not be overtightened.  You should remove them one at a time and put Anti-Sieze on them....every couple of months someone posts about breaking one off in the head.....it is a pain to get fixed.

Dave