I would drain the tank if you suspect a bunch of algea. It's still there, even if it's dead.
Just to put it out there: the algea lives in the water and eats the fuel. The water and fuel have similar specific gravities so there can be pockets of water floating around in the tank that might not drain like they would in gasoline. A little algea will be caught in the filter. A lot will clog up filter after filter. If it ever gets past the filter you're screwed.
If it is an air leak that's a toughie. It can run really well, then you turn it off and a leak that doesn't leak under pressure can leak under vacuum--siphoning all of the fuel out of the system and putting it back in the tank. My truck was doing that for a full year. I could not find a leak. But if it sat for over an hour, it would be a bitch to start. I replaced fuel lines all down the system and put a gauge on it down the line as well and couldn't find it--though I could watch it bleed down. Finally, on the advice of my neighbor who was a former National Guard Motor-T guy--I replaced the filter casting and the problem was solved. There was no pressure leak in it but somehow the casting itself was leaking under suction after the pressure was off of it.
Diesel are really bad motors to run only a few times a year. Better to have a gas pig in a grain truck. This former Guardsman bet me several years ago when I bought my 6.2 that the injection pump would fail before that Christmas. I won. He was used to Guard vehicles that sit all year so he was replacing pumps everytime he showed up for his drill weekend. In the marines, we used our trucks constantly and never had problems.
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