I have replaced most of what has been mentioned here, here's my opinion.
If you replace the header replace the downpipe, otherwise you won't get the full potential of the header. I went a week with my stock downpipe, found little to no gains with Banks header installed and Flowmaster 50 cat bak.
Took to Midas, custom downpipe and BAM, more pep, stronger pull, better sound from exhuast and I would guess better flow. Only thing, make sure you have a good look at the custom downpipe, mine didn't clearance the front drive shaft properly as it was fabbed on a frame lift so the axle was droopin... with it up, on the road it rubbed on right turns. Took it back and the repaired it, but just cut n rewelded it, looks like shiat now... buts still works better than that indented stock one.