"The 3 speed transmissions, either top or side, all had the same gearing ... "
There were 2 basic gear combinations, 2 Lincoln Zephyr combinations, and an unusual "Rule of 43" gear set.
Count the Main Drive Gear teeth (the top gear in the front of the transmission). !6 is considered standard, 15 is the equivalent of a Model A and lower than the 16, 14 is rare, but I have one. (18 and 19 are Zephyr combinations.)
A "1941 truck 3-speed" could be a variety of things. Study Van Pelt's site.
You do not say what engine you are using or where you live. Both could help in choosing the correct gears.
If you plan to use the transmission behind a Model A engine, the reinforcing rib could cause fitting problems with the Clings wishbone adapter.