You are taking the right approach--the condition of the subfloor dictates what happens next in many cases. If the floor is a total loss, then it is time to start planning the shell-off. In your case, it sounds like you might need only a couple of patches. So, I would recommend your next step to be to make sure that it isn't leaking--ie. check and replace all of the window, vent, plumbing stack, and door seals. Once you are confident that the trailer isn't going to continue to rot, you can work from the ground up--tires, axles, frame. Finally, you can get to work on the interior refurb.