I am #3 to jump on here especially if we are talking the trunk. Replace the entire floor and you will have a nice end result. I have done a number of them and patching in panels is just not the way to go. For a quarter or something where you have a lot more good than bad, then sure but not a trunk.
that said, if you are intent on only replacing parts/pieces, then replace EVERYTHING that is pitted or shows any damage.
Final thoughts, you are going to spend twice or three times the amount of time and energy to get something that is really not better off and will probably look far worse. I have welded a lot of panels and getting welded seams to disappear is very difficult.