Shop fee of $45??? Envrionmental charge of $45??? (WTF)
The fact is that your fuel guage is not working and is a direct result of the work they peformed on your truck's fuel tank. I would be leary at this point of the shop telling you that there is something else wrong (un-related to the fuel pump job they did) and it's going to cost you to fix.
Good Luck and keep your good eye on them...