It would appear you have an "algae bloom", which is a microbial growth that thrives in Diesel fuel. Unfortunately, a cleaning of the tank and load of fresh treated fuel is the only way to really clear it up. Dumping in a heavy 'shock' treatment of Biocide will kill many of the 'bugs' but may not give you the results you want. Firstly, killing the bugs does not remove their mass from the tank, so even after death they will continue to plug filters and pumps until fully cleaned out. Secondly, Diesel algae is absolutely insidious. It will live in the crevices in the tank and, if there is enough in there, may avoid the biocide and start growing again.
Drain the tank completely, If you can remove the tank, so much the better. Flush everything possible (sludge, solids, bacterial mass) out of the tank. Flush with either heavily treated Diesel, or gasoline. Remove and discard all fuel filters, then disconnect all the fuel line connections you can and blow/ flush everything out. Reassemble everything, then fill up with fuel treated at the "shock" dosage and get her running again. Drive it several times (dont let it sit for days if at all possible), then change the fuel filters again to remove remaining sediment/ organisms. If everything appears good, keep the tank topped off to avoid condensation buildup, and continue using biocide at the regular use dosage for as long as possible.
Ive used BioBor and Power Service brands before, but there are others that probably work fine too.
