Question: later model engine be adapted to a 2005 bike ?

You should be able to weld those mounts using the right gear....a mate of mine is going to weld up a hole in the case without pulling motor apart....he's been in the welding game many many years & reckons he can do it
I've seen his welding before & its impressive!!
 
I am not a welder
when i have had trans cases welded they set the cases broken area facing up.
so when they weld that section usually falls a little. so if it would be a prob u might need to stabilize it