I'm in the middle of a build right now & I think a few cost's werent included in your qoute , so heres the change order
Powervalve set $400
bearings $250?
seals & gaskets $50
Piston $200
Balance work $250? so it dont tear the case to crap again, intake boot $100 cause you dont wanna use the, 6year old at best, cracked one & chance sucking dirt or running lean, having your dome cut $150 while your apart, you want thermal coating on the piston crown, antifriction on the sides, total seal rings, etc....
My motor was junk, needed everything but the trans, & I might be sorry on that. I think the $3000 grand for new is a great deal for most guys, how many cherry cores are really left.
The conflict here is the custom built aspect will cost more than that $3000, reengineering what was done wrong in the first place takes hours & hours of skilled labor. If you have a motor built by someone whos reputable & knows these bikes I'd stick with it. Rebuilding it right being the key. Theres alot of details that really can be improved on v.s. just slapping new parts together.
I'd buy a new 450 sell the motor send them the just frame to mod & be money ahead though, most anyone can swap their own motor in & out with basic hand tools if you arent tearing the insides apart