To understand how Bio-diesel can affect fuel system you have to learn how it is made. It is not really a complicated process but understanding the different processes used can help you foresee future problems.
lye and methyl alcohol are used to bind to the fats and is separated out two ways, one is by letting it sit and it will form layers and you can drain the fuel from the top or the glycerin from the bottom. The second way or second step, is by washing it with water then letting it sit again and draining the once again separated layers. The water used can actually contribute to a change in PH of the resulting biodiesel because in the end even after letting it sit and separate there is still water emulsified in with the new "diesel" on a molecular level. The way to get the emulsified water out is to either heat it or filter it through water separator. Some say washing your bio diesel leads to problems with bio growth due to left over water still combined with fuel and recommend using settling and straining to remove the fats while other claim that it is far worse to put unwashed bio-diesel through your fuel system. Me personally i would settle, drain, wash, heat, and then filter it to get it as clean, dry, and pure as possible from all possible impurities.
