Ford boxes up thru 1942 were the dark green like the engine. I think the Merc boxes from 1939-48 were dark blue like the engine. The Ford boxes (and the engine) went to dark blue in 1946 til 48.
In 1949 I think Ford stopped painting the gearboxes but that could be incorrect. I have also heard that some assembly plants painted the gearbox and some didn't. Color (if painted) was black I think. At some point in the 1950's they stopped painting the gearbox altogether.
The 1932-48 inspection cover was chassis black. I believe the screws were unfinished but the bible would say. The shifter housing cover bolts were probably unfinished as hardware but I think they may have received the same paint as the gearbox color.
You may want to check in with the Early Ford V8 Club website for confirmation on these details.