Index the bellhousing to the tranny either by the outer diameter of the input bearing retainer (on a NP435, SM465, T5, etc.) or the input shaft bearing itself (by removing the non-round input bearing retainer to on a Toyota R151F, most aisin-seiko derivatives, etc.).

Or, if there's a bellhousing available, you can just swap it on, using the built-in indexing of the input bearing retainer or dowel pins, as above. This is definitely important, though -- if you don't get the centerlines of the crankshaft and tranny mainshaft to overlap their origins AND axis, you will fail either the input shaft or the bearings that suspend the crank and mainshaft. Making some form of runout check is good insurance...

Randii