Interesting you guys favor fitting the engine without the carbs.
As stevehot posted, a small jack under the gearbox is vital for ease of re-fitting. In addition the gearbox should always be supported anyway on early bays to prevent stress on the gear linkage coupling.
I fit mine with the carbs (twin IDF 40) and the mustache bar.
Wheel the engine in on the trolley jack with it turned at 45 degrees. Jack carefully up to the right height. This is so the carbs clear the body since they are a lot wider than the aperture can cope with. Rotate the engine on the jack to square it up with the box and then ease forward to engage.
The reason I do it this way is because its easier than trying to bolt the carbs and manifolds into place from inside the engine compartment. The trick is to go gentle and accurately. Only if you go at it like a bull in a china shop will you have risk of knocking bits against the body.
Although I do mine on my own, I would advise having two people if at all possible since it makes it easier.