Marc, what effect have the additional scoops made on the engines so far? I have to say I am sceptical of lack of air being the problem. I'll happily concede I could be wrong, but I'm still sceptical. The NACA ducts along the side are reasonably sized, plus having a pair of engines mounted behind a canopy or other obstruction is very common - look at almost any circuit boat for example.
If you are convinced airflow is the problem, IMVHO I would rig a few manometers to get a feel for what's going on:
1 in each engine cowling near, but not in the engine inlet
1 per engine outside the cowling, but inside the 'bucket'
If you find a problem, I suspect an internal mod either to the bucket or the engine cowlings to better control the flow would be rewarding.
Have you proven the 60mph figure without the bucket?
I don't think telltales will give you a correct view - there is going to be a huge amount of turbulent flow going on, plus the NACA ducts are going to have vortexes on entry - so it might look like they're flapping all over the places just because they're in a vortex swirling them around. NACA ducts are amazingly efficient.
How deep are the motors on the transom? I know before you've said they high, but how high exactly, especially in comparision to the race version (Do you have water pressure gauges fitted?)
Does it get on the plane easily and go round corners OK?
I'm also slightly surprised by the choice of prop - bravo 1's are traditionally a high load prop - a traditional favourite for a non stepped inboard powered V hull boat. Again, it might be that this prop has been proven to be a good choice - or it might be it was just whatever was on the shelf at the time.
I'm not familiar with how these boats run - do they like a fair bit of trim to get the bow up or do they run very flat?
I noticed the boat also has antifoul on it - IMVHO I think the effect of the antifouling could be signficant. On a boat like the B23 & V24 (I use these for comparison just because I've spend a fair bit of time looking at their undersides).
The steps role is 2 founded.
Firstly it aerates the water - this effectively lowers the density of the water and also controls the nature of the flow as well. I can't remember all the theory - it's about laminar and turbulent flow & boundary layers.
Secondly it provides pitch stability. By running the boat on 2 (or more) points, of contact in an efficient way, as the boat goes faster the pitch stability of the boat stays the same. It means the boat can work well across a very broad speed range. A normal V hull you have to keep moving the CG back (or trimming the motor) as speed rises which compromises low and mid range performance. It especially compromises pitch stability - I'm a bit worried about burty trying to do 90mph in his phantom since to make the boat stable at 90mph in the flat will, IMVHO massively compromise it's handling in any kind of chop.
Have you checked that you are actually getting WFO on the motors? It's possible the throttles are maladjusted and they're not opening fully? And that the ignition system is fully advancing the timing?
How 'clean' are the gearcases? I notice they've been painted - flow over the gearcases can be critical to prop efficiency - The ideal drive system for prop efficiency has nothing in front of the props, that's partly why arnesons are so good. If the drives are pitted you could start suffering blow out.
Refer to John G's comment about the race and pleasures boats running the props in opposite directions and higher X dimension - both areas worth exploring.
How did you achieve the 45hp figure? The Torque/RPM curve on e 2 stroke is typically very non linear, therefore for 15% rpm change it won't be likely to equate to a similar proportional change in power - probably a much bigger change in power.
Also, have you validated that the RPM gauges are calibrated correctly?
Please could you post the following so I can do some sums:
What is you current max RPM and what is the rated max rpm range for the motors?
What is the gear ratio of the engines?
What top speed have you you've seen, on GPS? (Was this in a tide/wind and what direction were they compared to you)
How much does the boat weigh?
What year are the motors and how many hours do they have?
Am I correct they are the 300PM and not the 300X?
There are 2 people who I would be interested to get some input from to explore ideas - Lorne, who of course designed the boat and Neil Holmes, who has had 'some' success racing Lorne's 3 pointer designs.

Matt