Same here, I put a new cover on and this new noise started driving me crazy, finally isolated it down to the intake, right between the heads. I cupped my hands over the open filter and the noise practically disappeared.
I may put the football cover back on to see if it goes away just to prove it that is it.

 

Exhaust leaks do occur sometimes. You could put one of those harbor freight stethoscopes on the heads to try and trace it down. Some exhaust leaks will start out sounding like that but they usually get worse as time goes on.

Do you have a solid lifter cam installed ? If so the lifters on those sound that way normal. If you do not have a solid lifter kit installed and your OEM hydraulic lifters are making excessive noise then their oil hole is likely clogged.

I have seen this happen on automobiles many times but usually it is after many miles or not changing the oil regular. Just in case you did not know it hydraulic lifters fill up with oil pressure on the lift cycle, to take up the required clearance in the rockers. If they get clogged they don't always fill up and cause this sound. Depending on how much clearance is occurring it can mushroom the bottom of your pushrods. Not sure what is the issue with your bike since I can't hear the magnitude of the problem but hope this info helps you.