You also need to have the battery disconnected when setting the trimmer to get 13.8V at the charger's LM317 output.
As for surge protection, if you have any varistors left over from the PDM builds you could put a respective one across each ~20V supply output. I don't think whatever you add (unless it's pretty expensive) is going to protect against a nearby lightning strike. Looks like you and KISS have got the GFI issue sorted.
Edit: The FPPMk2 has no provision for shutting off the pumps if the battery voltage gets drained too low when running from the battery. That shut-off feature could be added fairly easily, but of course would then mean that the water would stagnate. Which is more important to you: keeping the pumps going as long as possible, or preventing possible battery damage from over-discharge?