no, you want to mod the holes on the header side to mate with the cat. just copy the gasket to the flange and drill out the holes till they are slots going towards the pipe. you don't need a lift or the car even to do it, just the secondary part of the header and gasket as a template. you can also swap the belt before hand, just throw on a belt that rotates the alternator down to at least 1/2 of the adjustment. the + terminal is what hits the header if its all the way up. you can always move it to the bottom of the adjustment and throw on the appropriate sized belt for that before you get to tuning. all of this can be done with the car on the ground of course, so it would save time and precious $$$ at your tuner if you do it before hand. if you do it there you are going to waste at least 30min of trial and error with the belt, and another 10-15min drilling out the flange. that's 45min of time you can be tuning and testing.
you can pull the timing maps (the whole bin actually) through a consult cable if you are on a basic. im guessing your tuner is either has a dual ostrich setup, or has nistune ready to tune your car? without the aid of realtime, there is a lot of time wasted pulling chips flashing and putting them back to retune.