My boat is similar to yours in terms of weight and size, so that engine should push your boat at approximately 40 mph at WOT (6000 RPM) with the 15 X 15 prop, so you do have a problem. Attaining WOT at around 6000 rpm is very important for the health of these engines. Idle speed should be 650 RPM +/-50, so you are okay on that front.
Is this a replacement motor? If so, what did you have mounted before and how did it perform?
Simple things first. Try to eliminate items external to the engine before digging into that as the problem.
Are you sure your engine is mounted properly? If mounted too low, that could be your problem, especially with the 30 inch shaft. As a starting point, with the boat level and the cavitation plate level (trimmed approximately half way) the center line of your prop hub should be approximately even with the lowest point on your transom. If you have a motor extension off the back of your transom, then it should be
above the lowest point of the transom by one inch for every foot of extension off the transom. These are all approximates and can be fine tuned once everything else is operating properly.
Given your aggressive transom angle, are you sure you are able to trim up the engine properly? When you are on plane, the cavitation plate should be just skimming the top of the water coming off the bottom of the transom.
You said "engine tested good on the eng analysier prior to a 500nm shipment here." Was that with the Honda Diagnostic System (HDS)?
Any alarms going off - I assume not, since you did not mention.
Do you know how to pull the fault codes off the MIL? If not, order the SCS service connector (part number 070PZ-ZY30100 - under $20.00) and use that to plug into the 4 prong red service check connector and short it across the proper terminals to pull any fault codes off the MIL.
Finally, do yourself a big favor and spend the $115 for the Helm shop manual for this engine.
http://www.helminc.com/helm/search_service_owner.asp?session=48A505189F43457A8F10AC7E6420EDCE&Style=helm&class%5F2=MAR