even though the transmission is located by two dowels, i like to take a couple pieces of all thread and make a couple of long "pilot" bolts to put in the highest, easy to get to, bolt holes.
i make a screwdriver slot in the ends with a wizz wheel to make them easy to remove.
the pilots are easier [for me] to hit the holes as they are longer than the dowels. once the transmission hits the "pilot" bolts, the dowels come easy.
remove the pilots and install the proper bolts.
just something that works for me.