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In the old days, dealers installed the engines on the hull, not the factory.

Since 2000 owners and some dealers have discovered that engines can be mounted higher for better performance, less drag and better efficiency.

Typical installation used the "blind" holes for the lower bolts.

Your install is typical.

The repower installer was lazy and uninformed and re-used the lower holes instead of sealing the lower holes with plugs and epoxy and re-drilling the lower holes and then mounting the engine so that the upper bolts are in the 3rd hole counting down from the top. This would leave 2 holes open above the bolt. Hence, two (empty) holes up.

In addition the repower dealer supplied a cheap aluminum prop rather than the more efficient, durable and better performing BPR Viper 17" prop.

I would estimate as your boat is rigged, your WOT is ~37-40 mph rather than the 42-46mph. All due to improper install and poor prop selection.