It was the fuel

I figured out what was causing that awful hard starting problem and all those clogged fuel filters I had to change: I was getting crappy, low-quality fuel.

At the bottom of my biodiesel barrel, was a thick layer of sludge and grime. Unprocessed fatty solids, apparently. Disgusting. The guy who makes my fuel wasn't too surprised. Apparently that was in the fuel he was selling me all along, until he very recenly upgraded his equipment to use a better process.

Now that I'm getting better fuel, the hard starting problem seems to be dissipating. And the "WATER IN FUEL" light even goes off sometimes.