Where do you get your biodiesel from? What percentage blend is it? Is it ASTM certified? Using Biodiesel can potentially have some negative effects, especially if the quality is dubious. Biodiesel has the potential to coke up in high heat areas much easier than petro diesel. Also, it is my understanding that high percentage blends can affect timing as well.
I see that you have already sent your injectors to DBW for calibration. This is probably the most important thing you can do but needless to say something has changed. It might be worth it to send them back and have them tested again?
Good luck with the rebuild and getting things operational again. I spent a great deal of time and money putting an ALH into my vanagon and suffered a freak timing belt failure less than a year later so I feel your pain.
I always used ASTM biodiesel from certified commercial sellers. I would use anywhere from 25% to 75% (splash mixed). The main reason I stayed away from 100% was to avoid issues with chemical incompatibilities with hoses and o-rings.
Over this weekend, I had both my "new" PD injectors and my "old" injectors over at DBW. The main job was installing and balancing some PP1043 nozzles on the PD injectors. I also sent over the old ones so he could look for problems.
Pete was absolutely convinced that using biodiesel killed the engine. He thought the coking visible on the outside of the old injectors was enough evidence and was surprised that only two of the cylinders were blown.
I was going to look into it a bit deeper around here, but I found almost nothing about biodiesel in the alt fuel forum. Biodiesel is commonly available in various mixes in Oregon, and there's not some huge problem of blowing diesels. So, given that common usage, I'm still a bit skeptical.
Also, there are a LOT of other variables going on - especially in my engine.

Things that could lead to coking issues could be related to timing and amount of fuel injected. You'll notice from my sig line that a lot of this isn't stock. I've changed the tune, the injectors and the injection pump. The injectors weren't using OE VW nozzles, so there's a good possibility they had a role in this. The injection pump and injectors were installed (and timing can be affected) after the tune, so the tuning map did not take this into account. The engine seemed to run just fine, and EGT's were generally low, so I didn't worry about these issues until it was too late.
Does anyone have any links to solid tests about biodiesel and fuel injection? PD injectors subject the fuel to nearly 30,000 psi

If I use any biodiesel, it's going to be in small quantities. I mean, I'm a scientific type guy and I'd really like to see some solid testing on the subject. I really respect experienced opinions like DBW's, and will probably run with that in the end.