While I hate to get into these discussions about pinion angle
I do it both ways... but if I build the chassis and set the
engine/trans in it I go through a pretty decent set up.. I use
a laser that mounts into the #5 main(the laser has been trued to
the mounting block in my lathe) and I point the engine/trans dead
on to the pinion center line.. once the build is done I roll the
pinion to get the pinion angle I want.. so basically I use the trans
but when I check it from then on I use the drive shaft as reference