Cranker,
Oh boy...I think that the answer depends on the condition of your frame rails. If you have any rot in those rails and you cut out the inner fender, you might be asking for problems. You could also mount the car on the rotisserie, prop the front frame between the frame and the rotisserie, cut out the fender well and weld in the new one. Also, before you hang the car without a fender well, make sure that the floor pans are solid.
CODY,
Depends on how much quarter you're going to cut out. I can see how you could have the car straightened and mess it up if you were cutting out the enter quarter from the C-pillar all the way to the tail panel. On the other hand, if the rest of the car is solid, especially the floor and the frame rails, it should stay rigid when you cut out the quarter. If you have the car up on a rotisserie and you cut out the entire quarter, you might end up with some shifting that un does your frame work. Pulling on a quarter that was just install will crinkle the quarter. Pulling on a quarter that is crinkle will un-crinkle it.
I've thought about this issue in general a little more today. I'm not sure that there is enough published data to have the e-bodies lined up on a 3-D rack. Think about it, if you put the car on a jig, you have to have key dimensions in all 3 directions if you plan to get the car straight as per the engineering plans. The factory body manual has a very basic frame dimension diagram. If you were trying to get the car dead-nuts straight, you would put the car on a frame table (which is a steel-tube jig that is dead-level and represents ground level). Then, you would make all measures relative to that level ground and pull/push on the front/rear frame rails up or down to get the floor pan dead-level. The horizontal measures are easy. The vertical stuff would be more difficult as your frame rails, by design, are a different height above ground level the length of the frame rails.