Having removed the tranny twice in a few weeks, I can give you some advice.
If I where you, I will protect the frame with tape and install the engine first without the tranny;
Put a jack between the frame and put the engine on it on it's sump. Put the engine as far front as it will go. This will gives you enough clearance to insert the gearbox from left side without removing the swingarm. Then, using the jack carefully position the engine to align with the mounting holes, and insert the "screws" not forgetting the spacers if there are some. It is easier done than written and the jack is a blessing as it take all the load ! Then once the engine is bolted to the frame, finish centering the gearbox and bolt it to the engine. Afterwards, you have to bolt the shaft and the rubber boot then install cylinders, heads, carburetors..... And then run the bike !