Well, that rules out a throttle control issue so I would next be looking at fuel pressure and boost I suppose.
You'll have to forgive me, as it's been many years and my memory isn't as good as it used to be. I've only worked on the series 60 in trucks so I'm sure my knowledge is lacking as to boat installations. Such as intake air and fuel cooling configurations for example.
I'm sure I still have my DDEC III manual but I will need to dig it out to refresh and possibly develop some ideas for you.
Meanwhile, cover the basics...filters....water traps....fuel quality...etc...if you haven't already done so.