I don’t think that your water pump is protected. You have to plug it in somewhere, and the EMP will travel down the electrical cord into the pump itself, frying it. What you need is a spare pump and spare electrical cords, all in a faraday cage, preferably one that has multiple layers of protection. Either that, or have a manual pump available.
If I were in your position, I would go for the manual backup. Nobody here has considered the possibility of a second EMP strike several hours or days after the first one. This would catch a lot of equipment that had not been destroyed in the initial strike, and/or destroy spares that were brought out after the initial strike.
Thanks for the comment.