The loss of achieved rpm is mostly due to engine not being opt suitable for that boat, more hull drag to overcome fast + high altitude issues.
At just 3900 wot rpm you're extremely lugging the engine. Now imagine the extra poorer performance you would achieve under more load or + passengers. At least you count with an induction tach to know how well or not that engine is revving at altitude. Other boaters using same without a tach will be killing the engine extremely lugging it without knowing this condition is actually happening.
Go for a second wot spin as before, trim engine to be perpendicular to water level and move all the weight forward, see if by moving weight can make the combo to plane, if so rpm will raise accordingly.
A 15 or larger HP OB with factory delivered prop will perform much better than a 9.9, although not top as at sea level use, if you can't plane that combo and only getting fast displacements speeds, you are increasing hull drag difficult to overcome fast with an engine that's under rated and has already jets issues.
You can expect a 500-600 rpm increase per pitch decrease on a light combo at sea level, at altitude probably 50% increase in which case will need to decrese several pitch numbers to pull revs to 5850 with just pitch play. Anyway should achieve faster hole shot but with terrible top end speed decrease.
Happy Boating