As far as the BB goes, I agree with brmeyer, that sounds like something you'd have to do on an old steel frame, same goes for the head tube. I've built 4 bikes now (3 carbon road bikes and this IP-256), and none needed anything done to "true" the BB shell.
As for your fork, I recently went through the same issue. I left room for 1 small 5mm spacer on top in case I needed to raise it. I have flat bars and my stem is at -6 now. Worse case, you can always flip your stem and get riser bars if you cut it short and need something taller.