The header will not effect emissions.
I know that here in Pa. once you've spent "X" amount of dollars even if the vehicle still does not pass they give you an emissions sticker anyways... haha
What the dilly in the Delly?
btw What are your emissions readings?
You should have a print out that tells you exactly what emissions are at unacceptable levels.
I have a hunch that an obd0 B16 may be too "dirty" for some of our states laws.