I'll say it again, but typically pumps and injectors don't ever need to be replaced on Kubota mechanical injected engines UNLESS poor or wrong fuel is run through them. But people do it anyway because they want to be diesel mechanics like those movie stars on the youtube or tv.
But since you've already done that, I assume the injection timing is right. There ain't no adjusting the idle speed. They're wired in position from the factory. Actually the factory doesn't even give out the slow and fast idle speed specs on them, "adjusting" the stops also affects emissions so they tell everyone to leave them alone for that reason alone.
diesels rattle a little anyway but if it's an "odd" rattle, you may have internal engine problems of which aren't able to be diagnosed with any sort of precision without being there to see it in person.