I do the following with the bike on a floor jack with a block across the frame rails to the rear of the engine lower center mount bolt.
1) install the swing arm pivot bolt
2) Put the motor in (if it's out).
A) Put some rags around the frame both bottom bars (in front & back on center bolt holes & both lower vertical bars)
B) Put the motor in the frame
C) Installing the center bottom bolt so it pivots front to back
3) Rotate the rear of the motor down in between the swinger slots (grease EVERYTHING including the dust caps where the motor slips in between them) and get bolted up.
4) lower the bike frame on the jack so you can access the lower shock mount on the cushion lever and bolt it up, jack it up and bolt up the top shock mount.
4) lower/jack up the frame until it is around or just about above center travel and the cushion lever bolt hole should line up. Grease both sides of the dust caps that always help it go in between the swinger mount points. If you can not get the cushion lever to go inside the swinger it's ok to use a dead blow on the solid parts. And I also use a blunt punch on the recesses of the large center bearing to rotate it to get it to line up with the swinger/cushion lever mount bolt holes
Hope this helps