Let me try and respond to your question through the process rather than the finished product at the end of all steps since you will not be able to see much of it once the car is all assembled. This will get us to the same end just through one of a number of possible routes
1- Is the "cowl well" supposed to be body color or some shade of black? Hood black or engine bay black?
The cowl and well area would have been painted body color prior to any bolt on parts being added in that area of the car. During the period when you car was painted the black paint from the engine compartment paint application was not normally extended above the firewall to cowl pinch weld. That was done later in the production year at that plant in 1969
2- What color is the wiper motor and plastic cover supposed to be?
Wiper motor has a natural bare cast top or transmission section with a semi-gloss motor section. The steel bracket that attaches it to the car was paitned semi-gloss black before the rubber insulators were added. The plastic cover was unpainted black plastic
3- What about the mechanism that connect the wiper motor and pivot?
Those were plated likely cad but today many use zinc and dull it down a bit
So you have the body color cowl section
Was not unusual to have a small thin amount of black out applied to just the upper lip of the cowl panel to black out the area behind the VIN and gap around the dash pad
Once the hood and cowl cover were installed the hood black out for the Mach I and Boss package was done. This produced direct paint application to those items directly below the cowl cover grill openings and an overspray mist on the surrounding surfaces. It could produce a "tiger stripe" pattern on those surfaces such as the top of the cowl, wiper motor cover (the plastic shield) and wiper motor bracket.
Though not in black a similar pattern is produced (in this case in white) when a car was repainted later in life and the car was painted with the body panels in place. Ignore the black above the engine compartment pinch weld - this is from a later example
Hope this helps explain things