2-door XJs don't grow on trees, so if you're willing to go through the effort, more power to you.
The XJ only had one chassis and one wheelbase, so the floor pans and the headliner should be the same for both 2-door and 4-door. The floor pans are welded to the unibody "frame rails" with a series of spot welds, so you'll need to clean those up and grind the top flanges of the rails smooth before you start welding in new pans.
You are looking at a lot of work, so I would advise making certain you can sort out any engine issues before you buy the floor pans.