I am sure Carter must re-drill 1938-46 bellhousings for the later transmissions.
I believe The modified carter bellhousing is a 48-54 bellhousing that has been welded to accept the prewar brake and clutch pedals.
Rods 46, I'm sure you are aware that changing the transmission will likely force you to go with a new rear axle. There are many transmissions that can work with the 46 bellhousing with an adapter plate. Do you have a specefic transmission in mind? As stated above, the t5 is a popular swap. There is a tech article on this site detailing installation in a deco or prewar pickup. Below is a link to the tech article.
http://www.stovebolt.com/techtips/tranny/sandoval/index.html
