Have you tried replacing fuel filters. I had about 250 hours on my 496's and had forgotten to change the fuel filters in the fuel pump assembly on the engine. Did that and changed the plugs and gained my 3-4 mph that I had lost.
Great point. A slight loss if fuel flow is hardly noticeable on an efi, the computer senses ping and retards the timing and the boat keeps running like clockwork for a while but never getting full power as the flow has cost you a few degrees in timing.
If you have a scan tool you can watch the knock sensor and total timing while running the boat under load and see if the fuel is an issue