There are a variety of things that could be the cause.
- Did you turn the valve at the water pump back to the position needed to pump water from for fresh water holding tank?
- Do you have the same problem when hooked to your city water connection?
- The the valves in the correct position at the water heater?
- Is the any water pooling on the ground by your low drain points?
- Do you have the water heater drain plug in?
- Do you have the water heater overflow valve shut?
Vinegar has not been a problem for me when using it. I'm not sure why there is a clicking noise at the spigot in the shower. Here's a replacement on Amazon that may work for you if a replacement is needed.