i'm probably only stating the obviuos Rosco, but i'd bolt as much as possible together,motor,carby,airbox,exhaust,seat,tank {are there any exhaust mounting brackets you can use?},and chock it in place with whatever works, wooden wedges or temperary brackets. instead of putting bolts through the motor, i would try and use long lengths of round bar at first as the front sprocket is usually at 90 degrees to the engine bolts. you can square the motor up in the frame by measureing from the round bar {if that makes sense}. with another round bar through the swingarm pivot, it will aid in thos crucial measurements.
oh, and have a cold beer and some patience on hand.