When I put the car together I drop all the transmission parts together loosely. Just so the coubtersinks are seated but still allow a little movement with effort. Ill twist the car in my hands and check it for flatness on the board. Tighten top plate down a little bit. Repeat.
Ill also pull the belts to feel for binding/smoothness, wiggle bulkheads where nessisary.
Basically I start at the top and work down with the bottom bulkhead screws being last.
His video describes it pretty well.