Here's what I've found so far...
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You probably shouldn't have to too much modification other than replacing rubber fuel system components with Viton when you rebuild. Biodiesel eventually rots rubber.
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(regarding a GM 6.2 liter diesel) This is only in reference to the injector return lines that run from injector to injector.
A link to a discussion of injector pumps that have failed because of biodiesel use...
http://forums.tdiclub.com/showflat.php?Cat=&Number=661081&page=0&view=collapsed&sb=5&o=7&fpart=1
So far nobody has posted any pump failures, but I have heard rumors in the past.
So, based on what I've found thus far, you only need to replace your injector return lines with Viton lines (instead of rubber). Everything else
should be fine.