Specials from 1940-47 used a transmission with a short mainshaft and rear bearing retainer. From 1948-53 they used a long mainshaft and rear bearing retainer. Not sure the later type would fit into a 1940 model without major rework of other driveline components.
Attached are 2 pages from the 1940 shop manual showing the short type and 1 page from the 1952 manual showing the long type. The case looks like it's the same.