The one thing that I was told that will kill a 6.0 is a drop in fuel pressure. The injectors really don't like it when that happens.
Magnesol as stated before will go right through a 1 micron filter. I"m not sure how well a centrifuge will remove it though.
One very active topic on some biodiesel only forums is the use of oak shavings as a dry wash media. Yes, you read right. Oak shavings. I'm still doing some more research

on the subject while my truck is down with mechanical issues (doing the compression test today)

to see if this will be a viable and economical system for further purifying biodiesel. Plus the fact that the used up wood shavings would make a very nice fuel for a wood burning stove, you would only have to use a little bit to get the same amount of heat as a stack of logs.
As for the goo, I'm following the reasoning that it's a bacteriological infection. Sure looks like diesel blooms to me. I could be wrong however.
Have any of you pulled the injectors on your 6.0s and had them tested after you had this filter issue?