The transmission input shaft/output shafts centerline must be both concentric and coaxial with the crankshaft centerline. To check this, with the transmission removed, fasten a dial indicator to the crankshaft flange (a magnetic-base indicator works well) and rotate the crankshaft with the indiator plunger riding on transmission mounting bore in the bellhousing. The indicator reading should not be over .008". There's not much you can do to change this reading, as the bellhousing is located to the back of the engine by close-fitting dowel pins.
With the dial indicator still mounted on the crankshaft flange, set the indicator plunger to run on the rear machined face of the bellhousing and rotate the crankshaft. No tolerance on this reading is stated in the 1940 shop manual, but I would guess you wouldn't want to see more than .002 or .003. Be aware that the crankshaft may have some axial play in it that could affect your reading. Try to keep the crankshaft all the way forward or all the way back when rotating it. The runout of the transmission mounting face of the bellhousing can be negatively affected by grease/dirt/foreign material on the back face of the engine block where the bellhousing mounts. Make sure the bellhousing mounting face and the engine block mounting face are clean and free of any burrs or anything else that would prevent a complete metal-to-metal contact between the two.
When you mount the transmission to the bellhousing, make sure the mounting faces of the bellhousing and the transmission are clean and free of burrs.
Be sure the front pilot diameter on the clutch gear shaft is in good condition as well as the pilot bearing/bushing that it fits into. A sloppy fit here can cause problems.
Here's a link to the 1949-53 shop manual which describes a method of checking and adjusting the transmission alignment to the crankshaft:
http://chevy.oldcarmanualproject.com/shop/1949_53/07trans/7_010.HTMNote the section titled "High Gear Disengagement", especially section B.
This is a fairly rigorous procedure and requires disassembling the transmission. Disregard grinding off the teeth of the clutch gear. If you rotate the crankshaft, you don't need to rotate the clutch gear within the clutch disc. Also, disregard welding in a 1/4" x 8" rod in the end of the clutch gear shaft. A 3/8" rod just fits, and if you upset the side of the rod with a punch, it will fit tight enough in the hole in the end of the clutch gear shaft to support the dial indicator, but not so tight that the rod can't be easily removed when readings are completed.
One other thing to check is the transmission mount. With the mount bolted to the universal joint housing but not to the crossmember, the shoe of the mount should sit flat on the crossmember. If there's any space between the two, when you tighten the mounting bolts, you could possibly introduce some transmission misalignment. If you do have space, install shims or washers between the mount and the crossmember. I would check this first before disassembling the truck, because if this turned out to be the problem, you'd save yourself a lot of work.
