It doesn't matter what position the engine is in or what stroke you're on. Just match the direction that the locating pins point and your timing will be correct. If one pin points 180° away from the other, then your timing will be off.
The advance unit fits onto a similar locating pin on the cam end. There is only one hole for the pin on the cam so the only way to really screw this up is to leave the pin out. When the advance unit is mounted correctly with it's locating pin, that's what really establishes and locks in your timing. Then the advance rod gets tied into it with the little disc on the advance side. Unfortunately, since Yamaha drilled the pin hole all the way through the rod, the little advance disc can be installed in either of two positions. Only one will give you the correct timing.