the many revolutions need to align the timing marks is the mark on the middle gear under the case cove.
the T and the cam mark should line up every two revolutions of the crankshaft. with the timing marks off two teeth the noise would be from the valve is hitting the top of the piston. hopefully the valve is not damaged most likely it is ok since it is running ok.
yes the timing will need to be adjusted so the marks will line up and yes that should fix it when the marks are realigned. the cam timing mark may not be exactly on the cam mark. it could be a 1/2 a tooth off due to slight wear in the chain and chain guild system and that is ok it will work fine with it a 1/2 a tooth off.
if you need any more info I would be glad to help you.