There is a phenomenon refered to here as the "clunk", and a couple possible reasons and cures or not for it.
One is as you suspected the head bearings. Check the adjustment, you can find reference here if you do a search for "fall away". After making sure the head bearings are properly set, there was an update related to the steering stem and stem nut on later models.
Early models used an aluminum stem and later ones use a steel stem, also the later nut is flanged. Both items are an improvement but the stem can not be purchased individually but the nut can. You can check easily, there's a cap that screws onto the stem and covers the nut, remove it, only hand tight. There will either be a nut with tab notches and a lock tab (early type) ot a flanged nut without tab and notches. Thisis the one you want to have.
Also early Kelsey Hayes braked models, there is a bit of slop in the holes where the pad retaining pins fit. I find on my 04 that if you roll it forward and apply brake it makes a noise, a click more than a clunk, then if you roll it back and apply brake it makes the noise again. The pads float and stop as the holes limit movement, I think the bare aluminum fender amplifies the noise. Can't say this applies to those bikes with Brembo brakes.
"V" Rod Forman, '04 Anodized "B", 50th B-day gift from wife.
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