maybe the old diesel gelled up one of the fuel lines? or a couple? or one injector is clogged up? pump seems unlikely to me too. but a couple of hundred for a test isn't really worth it I guess. it's a bit of a gamble this one. if you manually accelerate the engine and hold it at the point where the vibrating stops, (1000rpm or so) it'll start vibrating again a few seconds later. if you then pull it a little further, it will stop vibrating and start a little later again. that was odd.
but serious, that engine doesn't like idling! the rubbers it sits on are wasted. and it felt like it would explode when stopping. and even if you do get it fixed, would the damage be serious on the one cylinder that didn't get any? I'm sure it hasn't been driven much in the state it's in. I can get an IP at pull a part cheap, with 300k miles on it.