i've never tried to do it with the motor in the frame becaue its not a lot of extra work to get the motor out. pull the fenders, drop the exhaust and a few misc wires and bolts and it pretty well slides out. yamaha did a good job designing it i think because it can be pulled in a half hour or 45 mins if you work fast. i think the hardest part is just gettin the airbox and carb out, after that, its a snap.
as far as building it is concerned, have you decided what you are gonna do to it?
"The Cowboy"
'96 built to the hilt warrior
cardomain.com/id/glass_cow