"Although my Blog post is about the 1940-54 transmission, as they are the most common to have this problem, the same applies to your trans."
Dave,
That's great information on how to verify transmission case alignment! Obviously it takes some effort to mount to mount a "last word" type indicator in the input gear as you have done but your method will absolutely facilitate perfect alignment.
Many shop manuals I have seen state that "jumping out of gear" can be attributable to the exact misalignment your information addresses.
Replacing gears and/or synchros in a misaligned transmission will cause the same uneven wear on the new parts and jumping out of gear problem that the parts replacement is trying to correct.