I am not running homebrew biodiesel in my CRD, but I am a chemist, and have made it and run it in a Jetta TDI without incident. I am currently buying commercially made biodiesel, although I'll probably build an appleseed processor at some point.
I added enough of the commercial biodiesel to the tank of the CRD to bring things up to a 50/50 blend with the 40 cetane crap the dealer put in it, and I can tell you that it made a huge improvement in the sound of the engine. Not to mention it's exhaust smell!
I'm kinda cautious of my rides, and plan to not take the CRD over about 50% for a while, to let everybody else determine if the higher injector pressures in that common rail system play well with biodiesel before attempting to run 100%, like I do in the Jetta.
But then winter is coming on, so I'll probably be running 50% in both during cold weather. Ask me again in the spring . . . .