Let's try to do some failure analysis. I used to break input shafts for a living when I worked in the Test Department at Allison Transmission, so I do have some experience in this area.
Did the shaft break into two pieces? If so, look closely at the formerly mating surfaces. If the shaft broke from pure torsional shear, the entire surface on both pieces will be rough. However, if you can see where part of the surface is kinda smooth while the rest is rough, then the break started at the smooth area. If the smooth area is near the surface of the shaft, then there was some defect at the surface that started the crack which lead to the failure. The defect could be a stress riser left by machining, or a stress riser left by the hardening process, or a stress riser resulting from a material defect. You may see "beachfront" waves across the shaft--this is an indication that the shaft was cracked for a long time before it broke.
If the shaft is just cracked, not broken, then you can look closely at the crack to see where it started...usually at some stress riser. We used to do a lot of dye penetrant testing in our fatigue testing lab because it was quick and did a decent job of showing surface cracks. You can buy dye penetrant kits and I'd recommend using one periodically on parts that are subject to fatigue failures so you can see the cracks before you suffer a catastrophic failure.
Bear in mind that a shaft loaded in torsion is very dependent on what happens at the surface of the shaft. The stresses are greatest at the surface. That's why hollow shafts are used in some applications. Hollow shafts have almost all of the strength as a solid shaft, but you save some weight.
Torsional fatigue generally isn't a problem with the transmission input shafts on small cars. The loads are just not high enough. On the other hand, when you are getting 400 horsepower out of an 8-cylinder diesel engine that's only running about 2500 rpm, the torsional stresses passed to the transmission input shaft are massive.
As someone else said, make sure you use the dowel pins between the engine and transmission as they do most of the alignment, not the bolts. Any misalignment in this area will be hard on input shafts and bearings.
Bob...