Re: EEK! They've taken the sulfur out of Marine Diesel!
When they switched over cars the main failure mode was that the seals in the pump would shrink. Years of using high sulfur fuel had caused them to swell and then the low sulfur fuel (and biodiesel, which is naturally low sulfur) would allow them to shrink, destroying the seal. There were replacement seal kits made for popular pumps (like the VW TDIs that are everywhere in Seattle) that would let you replace only the seals and do a light rebuild and get it working nicely again. Of course the dealers and many mechanics didn't offer this and would only replace the fuel pump, but many of the independent shops were doing the rebuilds.
I expect that it is primarily the same failure mode at play here, but don't know if there are replacement fuel pump seal kits available for the popular engines (like the Yanmar 2GM20F on my boat).
One fixed the fuel pumps worked just fine and lasted a long time. It also wasn't universal, at the time of the switchover my wife and I had two VW TDIs and I was helping friends with 5 or 6 more of them. 2 required fuel pump service, the others never had a problem with the switch.
1986 Pearson 28-2 "Elena"