I'm not 100% sure about this because I have four door and I'm not sure what you are asking for but behind the rear wheel(the rear quarter) the two door and the four door should be the same and you should have no problem following a write up that used the four door. If you are talking about cutting the wheel wells for more tire clearance, the two door would still have the pinch seam to deal with. If you are willing to cut past the pinch seam, you should be able cut the fenders larger because you don't have the back doors to deal with. If you do cut past the pinch seams, you are going to have to make new inner fender wells and all that jazz.
Maybe somebody with some experience on two doors could chime in.
Chris