For most of that I'd check with VMP tuning in FL, he's (Justin) done a lot of similar changes, Might want to check out Fnsweet.com for others with Roushs and good info. When I was out at their plant, asked them about headers when increasing the power and they said for what you pay, not really worth it. With the other supporting parts, you might be getting close to the limits of that stock bock anyway. Former 427R owner.
2015 Stage 3 Roush
'66' Ranchero w/almost done 302 T-5 swap
2000 4x4 Ranger
2003 4x2 Ranger
'69' Fairlane Cobra, 428 4-speed waiting for work