I bought 2 dead Mazda Capellas from a biodiesel guy; sitting 8 years. He had started out doing all the right things then stopped using a biocide. One car had to have the whole fuel system replaced, filled with bitumen and the case hardened parts were too corroded to use even when it was cleaned up. The other had a dead motor, no head, cylinders filled with rat piss and detritus but for fun I opened up the fuel pump and it was pristine so I swapped it and the fuel tank over. A diesel mechanic told me how to clean these things. They have to be stripped down. They use a bronze wire wheel and acetone on the steel parts which don't like water and an ultrasonic cleaner (with water) to clean the aluminium housings. You should not use caustic in your fuel system as it will react with aluminium. To clean the fuel system in situ and keep living organisms out of your bio use Chemtech diesel treatment just like was in car #2, a litre costs about $30 at Super Cheap Auto. Put 200 mls in each 200 litre drum of fuel and the bottle has a handy squeeze measure system and you won't have to get any on yourself. If your fuel has been properly washed and dried your troubles will be over.

Although I was getting some black in my wife's PD Caddy van. It seems the individual injection pumps (one in each cylinder) are lubricated with engine oil and some leaks through into the fuel system.