It's tough to advise if the noise is 'normal' or 'not' sitting here at the keyboard.

If you haa come from a water-cooled engine then I'd say that you are just not used to the noises an air-cooled engine makes.

Having ridden an HD I suspect you may be used to 'noises' so ...

Get yourself a stethoscope. Listen to the top end. Even thought the valves were 'checked' they may still be out a bit (you said it clatters) and that's where the majority of the 'non-regular' noise comes from. Check the lifter (bottom of V, right side) and alternator (right side, by foot) areas.

A high pitched sound from the left side may be the belt .... it's too tight. Grab the bottom of the belt (halfway between the pulleys) and give it a turn; you should be able to turn it about 1/8 - 1/4 of the way. Try backing off the axle adjuster 1/4 of a turn and see if it goes away.

Doc