I'm not sure there's a specific way of building your bike. Depending on what type of riding, maybe beefing up the suspension might be first. If you ride through dunes/open fields maybe engine work is first.
Depending on who you send your cylinder to for porting, talk to them and see what they think as far as an exhaust system for your set-up. After all, they'll be the ones building your engine. As for porting, I would highly reccomend Herr Juggs Racing in CA. I've had Kevin do 3 bikes for me. Amazing work and fast turn around.