The carbs will just get in the way. I would install the head, set the motor in the frame, put the gearbox into the cradle, bolt the cradle up to the motor, then install isolastics. But that is just me. Most assembly processes have at last one advantage and one drawback. I can't say I have ever built much of anything that didn't have to come apart at some point because I overlooked something obvious. Go for it. The worst case is you get to do it over!
As long as it isn't inside the case, the process is usually not that painful.
Russ