I took a look at the tranny from my '48. It doesn't look like the forward torque tube retainer on the transmission (the 'keeper' for the torque tube at the rear transmission interface) is part of the lubrication for the driveshaft forward u-joint... so you should be good there, as long as you can locate a u-joint with appropriately sized cross.
I can see two issues with changing your factory '42 rear with a '64. First, the leaf springs are not interchangable due to the factory '42 torque tube configuration. The axle on the '42 is not bolted to the leaf spring pack as with 'conventional' axle installations; the axle is attached to a bracket that is in turn attached to the leaf spring pack. This allows the axle to have relative motion to the leaf spring pack, 'hinging' about that point due to the torque tube style design. So you'll need replacement leaf springs.
Second, you'll need a replacement drive shaft with fixed yokes at both ends and a slip joint in the tube itself. This should not be a problem, as many Jeep rear driveshafts have been converted with a slip yoke eliminator that requires the exact same style of spline in the driveshaft between the u-joints.
There's nothing wrong with the factory '42 design that I can see from an engineering standpoint, so why are you wanting to change to a '64 axle?