Myself when dealing with a manual trans I either
1. pull the shifter off the trans ( assuming it's a 4,5 or 6 spd)> pull the Z-bar & clutch linkage. Drop the driveshaft and either shove a spare yoke in or drain the trans> then proceed to pull the engine & trans as a unit.
or
2. Drop the trans from underneath.

IMO, trying to line up the input shaft on the trans to a motor hanging from whatever is asking for trouble. others may disagree and that's fine