You are right where I used to be, couldn't make the correct RPM at WOT. So, as was said, open the throttle in neutral and make sure you can turn 4000 to 4080 RPM, the maximum RPM he QSD is supposed to spin and if you can't make that RPM underway, you're probably just over propped, which is acknowledged here in the TugNuts; these boats were over propped from the factory and that gets worse with the "equipped" weight we load them to!
In my situation, after my neutral performance check, I read the label on the ECM to ensure the ECM had been updated and then had the ECM read by a shop both static and under load. Once I confirmed the engine was operating as it should I had the propeller depitched a pitch at a time going to two depitches total which is the maximum I'm told a propeller can be depitched, (also had it de cupped a bit) and I gained about 300 RPM per each depitch which was also what I was told would happen and my load and throttle percents kept getting closer and closer but still no 4000 at WOT.
Then I had to step back and take a breath because at this point my propeller guy, Acme and Andrew were all telling me what I'd had done to the prop should be producing better results; they all said weight, weight, weight. So I took all the weight off, I fish and dive and the weight that came off was a lot! I went back out and spun right up to 4000. I put some weight back on and finally had to have the propeller reduced in diameter 1.5" to regain the proper RPM at WOT with the boat loaded to my needs. And that's really all you'll be doing, propping the boat to make the correct RPM at WOT at its current weight so you don't lug the engine throughout the entire RPM range.
Looking back, some things that the owner of the shop that read my ECM told me gave some perspective: "Remember, you're not exactly loaded with horsepower to begin with: how many 25s do you see out there with twin 250s pinned to the back?" "Also, these light weight, high output, (we are getting 150 horsepower out of 122 cubic inches) high RPM, (4000 is really spinning a diesel!) marine diesels don't have the "shoulder" (torque from internal spinning mass) that you expect of diesels." "Look, in your mind take the engine out of your boat and pin a 150 horsepower outboard to the back and realize you'ed really have to flog that outboard to get anywhere near the same performance and it wouldn't last anywhere near the hours of service you can depend on that diesel to go."
That last one really resonated with me and as it's said throughout the 'Nuts, "it's the journey not the speed." So now I can make 4000, I operate at 3200 (80%) and I don't care what my MPH or GPH are because at that RPM they are what they are and I can't change them, I open her up every now and again to blow out the carbon, stay up on my maintenance to ensure that diesel dependability and life is good! Hope this has been of some help. rich
