I would suggest doing the trunk floor first. Then the extensions and drop-offs. This way you can take a bunch of measurements before you start including a couple on the diagonal. Make measurements from what ever solid metal you have left on the original parts. Mark the measurement points on your new panels so you know you are starting out OK. I would tack weld the trunk floor and components well enough that there is no chance they will move out oof position, Then do one quarter panel at a time also tack welding. You should be ok then assuming you used the measurements and reference points from the original panels. By tack welding to get everything lined up you should be able to undo sone welds and move things if need be.