I don't mean to insult you, but are you sure he got it from tap water? The only two people known to have gotten it from tap water were two neti pot users, and the amoeba was not fount in the city water pipes in their street, only in their house. That means in their plumbing, somehow the amoeba was getting in, possibly through the water heater. City water is chlorinated and that kills the amoeba. There were special circumstances that allowed the amoeba to grow in the neti pot water, which are not known.
In your case, I would actually recommend that you have your water tested for the amoeba, I'm not sure where you would get this done, I suppose there is an independent lab somewhere that does it, or you could call your county/state health department or the CDC to find out where you can get your water tested.
You could also have your plumbing inspected for any leaks or places that anything can enter the pipes, any maybe have your water heater replaced if it is old/dirty/not in good condition.
I know all of these are all drastic measures to take, but it's what I believe needs to be done to get a handle on your life and to start living normally again.