Mike, I am going to assume that you can get to high idle speed with the engines out of gear. Is that true?
First I would verify that the throttle cables and linkages are intact and adjusted correctly, and that the racks are opening all the way when the throttle levers are at maximum. Also, you would want to make sure that there is no restriction in the fuel supply to either engine. All these things will keep the engines from reaching their rated revs under load.
Next, I would check your engine revs with a phototach, if you have one available. This makes sure your tachometers are not lying to you, although they are probably okay.
If you think the problem is excess weight (and a small boat like the Series I 36C is weight sensitive), then you might try taking moveable weight out of the boat (fresh water, furniture, etc etc) and seatrialing it again. If lightening ship restores your performance, you may have the answer.
You don't mention whether the boat previously performed as it should have and then lost performance, or whether it was never right to begin with. That is significant, potentially because if the performance was never there, there may be something fundamentally wrong that will prevent you from reaching your goal no matter what you do with the props. One of our forum members, for example, found out that he had been sold two different ratio ZF gears by J&T, so the boat NEVER would have performed properly until that was remedied. (To their credit, after some phone calls to Mr Johnson, they stepped up and replaced the gear with the wrong ratio with the proper one.)
The absolute guru of Cummins diesel performance is Tony Athens at Seaboard Marine in Oxnard, CA. He is also the moderator on the boatdiesel.com forum. You should join that, if you have not already, and post a thread asking about this. He will likely have plenty to say about this. Tom Slane has also repowered four or five of these boats with 330Bs, some with 1.5 ZF gears, and he will know quite a bit on this as well. Between these two guys, you should be able to find your answers.
I think the bottom line here is this: you are on the right track seeking to get proper EGT and boost figures, coupled with getting the engines to turn up to rated RPMs at WOT, or even a little higher. If she can't do that, and the throttles etc are opening up all the way and the fuel path is not restricted, and you don't have excessive back pressure choking the turbos- all those kinds of things that hurt performance- then the engines ARE over propped. I am surprised, though, because with 1.5 ZF gears and 330B engines, you should be able to swing larger wheels than that. Are the wheels actually what your prop shop says they are? You would not be the first boater to find that the props were mislabeled. By the factory, which has happened to me.
My boat has 350hp 3116s, which are not identical to your engines as they weigh about 300lbs each more than the Cummins Bs. I have 1.5 ZFs, and run 21.5x22 Michigan DQs. Rated WOT on these engines is 2850 under load, which they will reach. At those revs, she is doing about 28kts. Cruise is 25 kts, at about 2500 revs. I should mention that Blue Note is probably lighter than your boat, leaving aside the question of engine weight- I do not have the extras that you do, and I typically run with only 30gals water or less and prohibit fat people from boarding. I have gone to a fair amount of trouble to get weight out of the boat; as you know, things creep aboard and the weight creeps up.
My apologies for the lengthy post. I hope this is helpful.