Just my opinion here, but I believe the running boards were always black. They were on the AD series trucks. Fenders would be the same color as the body. And I believe like you, the body color wheels with stripes would have come from cars, which used the same wheels as the trucks. Truck wheels would be black without stipes, although in later years, the deluxe model trucks may have come with body color striped wheels.
HERE is a link to the Vehicle Information Kit for 1940 trucks.
And for body colors,
THIS is a good resource. The green you're seeing is called Brewster Green, and was likely the standard color for pickups.
