Kelly Bustard

I need a new muffler and donut gaskets (AKA exhaust gasket)... I am also trying to decide whether I should replace the exhaust manifolds or get headers. When I first took my 86 F150 through emissions a couple months after I bought it two years ago it actually blew all zeros but the gas cap failed.... after the gas cap it blew 00 and .002 on the two scales. They were amazed at the numbers saying that the truck was very well cared for over the years... Could headers made that much of a difference that the truck would fail after posted near zero numbers two years ago???