after my longtube install this question daunted me. well, i WAS TOLD that if you take the shifter off, you can rotate the trans 90 degrees and slide it right out. granted that seems to be a pain in the a** to do that with your car on jackstands, i think i would rather do that than unbolt a header.
But like i said, that is what i was told, i have no proof that that works
dirvers side header is fine, its the passenger side header that gets in the way. i loosen the header enough to swing it out of the way. if you are running an aftermarket k-member, just take the header out.