Just cleaning and flushing isn't going to get rid of the diesel bugs, as you've already learned. YOu have to clean everything ruthlessly with brushes and pipe cleaners and scouring pads and lots of changes of solvent and then treat everything with HUMbug biocide and let that sit for a while in the whole system. After that you can refill the fuel tank with new, clean fuel that has been treated with biocide/HUMbug preventative. YOu will need to similarly clean and treat every fuel container you use, funnels, hoses, etc. It only takes one (1) live HUMbug to start a whole colony – it doesn't even need a girlfriend to reproduce, the little deviant.
Bob Rooks is the resident expert on dealingwith HUMbugs; hopefully he'll chime in here and add anything that I have missed.
Rich