3TNV88C Tier 4 Rail Pressure issues

Hey all, So I'm posting in here since I think the 3TNV88 engines are pretty popular on mini-exs. Mine is actually on a portable sawmill. Anyways, I (stupidly) filled it up with dirty diesel this week, and the little computer on it started throwing codes almost immediately. The codes I'm consistently seeing are P1668 (rail pressure too high during PRV limp home mode) and P0093 (rail pressure delta value high). I can crank and start the engine just fine (as long as I shut off the ECU for a few seconds), and it runs for about 10 seconds until it starts throwing those two codes again. The engine hiccups, runs for about 5 more seconds, then shuts down. (The service manual says P0093 fault mode is engine shut down, so this makes sense). Anyways, I'm looking for advice on what to look at. I replaced both fuel filters. The secondary/water sep was filthy and had gunk on the 'clean' side, the primary filter looked fine when I dumped it, but I replaced it anyway. I removed and cleaned all the feed fuel lines with compressed air. Emptied the tank and put clean fuel in. Tested the electric lift pump for steady flow and it works. I removed the suction control valve (SCV) from the supply pump and the filter screen on it was clear. I plan on calling the yanmar dealer an hour away tomorrow, but who knows when they'll be able to see it. I'm losing money every hour it's down, so hence I'm hearing looking for more advice. Thanks, John