I thought they were unpainted, zinc plated. No paint on my 65 and at least one of my 66's.
Some items were not attached to the engine when it was painted, and added later.
The cast aluminum alternator bracket (non AC) was unpainted, and the 2 head bolts may have been too. It apparently was attached after engine was shipped to the assembly plant. Both the steel alt support brackets on my '65 were unpainted. On my 66's they were either black or red.
Fuel pump on my 65 had overspray on it, so it was attached when engine was painted. Suppose the rubber lines (and filter) could have been put on before or after painting.
I wonder if the assembly manual has any details on fuel line lengths and filters. If it does, they were likely added at the assembly plant and not at the engine plant..... and would not be painted engine color.