If you've lost the original waterline, it's going to be difficult to re establish it in the correct place. I'd think you should sand off the antifoul before you start painting, and probably should have kept the water
line masked or marked all along.
If the boat is level (also tricky to be sure of) you can use several tricks to lay out a good
line. A transparent water hose can be used as a level guide, or nowadays a laser level tool can be used to generate your new
line (but the laser tool has to be on the same plane or level with respect to the boat on both axes - for and aft and athwartship)
Perhaps if you can find a sistership you can take some measurements off of it to re establish the proper
line.
Once you've found the
line, do your topside
paint and then follow up with a boot stripe of your choice.