[Banshi]

I think if the tank can be removed fairly easily I would do it and clean it out, otherwise I would just keep a close eye on the fuel filters and water separator if you don't have to change/drain them every other time you go out I would just let them do their jobs. I think putting additional holes in the tank just introduces another possible source of contamination.

Once the water separator reaches it's limit the engine will shut off and run no more until it is drained. Water does not compress well and can cause serious damage to the engine . The fuel filters on diesels are much finer than those on gas engines so they can clog fairly quickly as well but it would give you warnings before it shut off with a loss of power and poor idle.