Hi, I'm pretty sure P.U.M.P. code assume a resource is 1x1 (like the oil wells are). So I have no clue what a Fumarole is, but if it's a 4x4 source, I'm pretty sure that has to do with the problem.
Would you be so kind to provide a save-file as well, so I can quickly reproduce the issue and test with it? I don't like doing alternations for specific mods. But if I can find a more general improvement to cope with the scenario I'd like to give it a try. It sounds pretty 'away' from vanilla, so no promises.
As for the Pipe 2, .. a quick guess would be that it does not have underground pipe, or it does, but it's not named according to convention like in the vanilla game.