Hmmm, I've had some similar challenges on my Cub (also a 3-cyl mitsubishi diesel). I put old junk diesel with 20% bio in my fuel tank ONCE, and have had some problems ever since. Even rounds of biocide and additives have never gotten it all the way back to normal (I'm too lazy to pull the whole tank and wash it out, so far). But thankfully for me, a clean fuel filter will give me at least 50 hours of good running.
It sounds like you could have an additional issue. If your fuel filter is not obviously clogged, plenty of diesel should be able to get through. My filters get totally packed with slimy crud before performance starts to fall off. So you likely also have A) a weak lift pump, B) a partial clog in a fuel line, C) an AIR infiltration leak, or hopefully not D) a problem with your main injection pump up on the motor.
A relatively easy thing to do would be to upgrade your filter housing to something larger, with less vacuum/obstruction, and a bigger lift pump with a couple more PSI.