for now at least change your fuel filter, see if that immediately helps. If it does you probably did not filter your oil well. If you are going to stick with this set up, go with a 2 tank system as the others mentioned. Try to find a better filtering system. On the diesel side 2 microns is top notch, doubt if bio would ever flow through that, maybe if it was real hot, and well filtered already. I have read that you can buy 10 micron filter bags and you put 25 gallons of fuel in one suspended in a 55 gallon barrel, the clean oil will trickle through eventually and leave most of the crap behind. Then this stuff in a heated tank going through as fine a filter as you can afford to replace regularly should work pretty good.
I suspect even if you dump your tank right now unless you change your fuel filter you wont see much improvement, you may also just need to drain the fuel water seperator. Best of luck, I admire your creative adventerous spirit. I have done a lot of reading about it and I havent the guts to try it yet. Probably wont, but might try making a batch of bio.