Back when I was shopping for headers I saw that several, depending on part number and manufacturer, indicated there would be interference with the column shift linkage. I've also read about guys having to 'tweak' the linkage to make it work with headers.
Otherwise you have a few options. If you wanted to go with the factory floor shift, you would still have the linkage between the trans and the column to contend with. That linkage is there on a factory floor shift for functionality of the neutral safety switch, the back-up lights, the ignition lock cylinder interlock and the instrument cluster mounted shift indicator. When the floor shifter is moved, the mechanical linkage causes the lower 'collar' of a floor shift column to rotate just as it would when you move the gear lever on a column shift. If you wanted to go with buckets and console then you could do so without pulling the transmission. The mounting brackets for the console and the inner seat mount brackets for the buckets are spot welded to the floor board from the inside. If your car has a split bench then the inner seat mounts for the buckets are already there.
The easiest thing to do would be to find a different set of headers that will work with the column shift linkage and have your exhaust shop modify the very front portion of the new exhaust system to fit them as necessary.
Otherwise you could put in an aftermarket floor shifter either with the bench or with a pair of buckets. You would either have to be able to move the neutral safety wiring and back-up light wiring to the new shifter or you would lose that functionality. Your shift indicator in the instrument cluster would no longer function. There are aftermarket shifters that have their own shift indicator. You would need to remove the column mounted shift lever, decide to live with it or change to a column shift column.
No matter what you do, if you can't make the linkage between the transmission and the column work with the header, you will lose functionality of the ignition lock cylinder interlock. You would need to 'immobilize' the collar of the steering column in either the park or neutral position so the ignition lock cylinder will move freely from the 'lock' position to start, run and accessory positions. The downside will be that it will then be possible to lock the lock cylinder (which locks the steering wheel) while driving the car.
Hopefully this will help you make a good decision on how to proceed.
