It sounds like your elements may be hooked in series if you have 120 on them. Or maybe it is a 120V unit. That is why I asked for a model #. But why they had 240 on them don't make sense. Unless you were working in your breaker panel wiring your new water pump. If the new thermostat is wired wrong, that could cause 120, but you would need to be swapping wires. Also some units may do that for efficiency. Model maters.
I am clueless at this point. But still suspect the top element if no wiring was changed. Because of the fact that it may have been on with no water to cool it.
Just make sure your Pop Off Valve is good and has a place for the water to go.
Sometimes it is best to download the manual for what you are working on, Before you start working on it. Then You can understand how it works, and be Safe working on it.
Water Heaters are really fairly simple if you know how they work.
For safety reasons if you do not know how they work then you should not work on it.
Read your Meter manual also, so you know what you are reading and measuring.
If I am wrong then please tell me, in a PM if needed.
Terry's site has good info, But He and Myself like for everyone to be safe when working on a DIY project.
I'm really paranoid that I wired something wrong now. The model is a Rudd ET-40.