Gorgeous truck by the way: 54 3100 5-window. I love that paint job! As for the transmission; it's very possible that someone transplanted a later SM-420 case and guts with the original tail shaft made for the torque-tube. You can install the 3.55 gears but a 54 3100 has 3.90 gears already. Right? 53 was last year for 4.11 in 1/2-tons. Did you run the differential number?
Correct me if i'm wrong about the 3.90 in 54.
I looked it up: 3.90 rear gears in 1/2-tons started in 54
http://chevy.oldcarmanualproject.com/shop/1954truck/54ctsm0447.html By the way, I built a 235 from parts of at least 4 motors for my 55-1 3600 and it had a 53 head on a 56-62 block. A lot can and does happen over 50-60 years.
Good luck
