Loose or worn out wheel bearings.
Easy to check, grab the top of the wheel and rock it back and forth, listen and feel to/for clunks.
If it has a sway bar the end links and supports could be warn out or missing.
Jousting the front end could recreate the clunk,
Turning the steering wheel...
Here is the 67 headrest internal parts.
https://pgclassic.com/products/810buk-67kit
Here is the 68 kit
https://www.classicindustries.com/product/1969/dodge/dart/parts/MD2047.html
They may be available at other resellers so check around.
IMHO
Only putting a factory OEM manifold on with gaskets and bolted down to check for alignment is a valid test.
Also as a control looking at the fit between OEM head and OEM intake with gaskets and bolted down is needed to make the claim that the head's ports are off.
OR OEM engineering...
My OEM 67 one family Dart did not come with the black cup that locates the hard board cover. It may have been a Plymouth thing or 68 up?
Maybe it's the wrong one?