Do you need to take off the cylinder head cover to perform a leak down test?

 

Yes -- the valve cover has to come off so that you can verify TDC by the cam alignment. Even a couple degrees off will make the readings garbage. As a side note: most bike valve covers are a bee-yatch to remove. Usually the throttle cables and a slew of other goodies must be removed to get it gone. On some models it's easier to remove a couple of engine mounting bolts and tilting the engine down to remove.