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You seem to have done everything recommend correctly, yet still the engine RPM/Propeller pitch/speed number do not calculate correctly. The engine should turn closer to 5500 RPM, and with a 20" prop, you should be getting 40-42mph
considering the boat is bottom painted. Paint DOES hurt top speed.

This leads me to believe one of two problems. Either the engine needs work, or the boat is heavier than it was originally. Do you know the history of the boat, such as has it suffered damage and been repaired? This can often add a lot of weight, as fiberglass and polyester resin repairs can be heavy. Bottom paint is often used to cover up major hull repairs. A trip to a weight station might be in order. To me, in your photos, the boat looks heavy. Maybe just my crazy observation! I have a Montauk 17, which I know to be all original and correct factory weight, and with a Mercury 115 does 50 MPH. A friend has one with a Mercury 90, and it does 43, both boats without bottom paint.

The engine also needs to be looked at, as many things could cause it to be low on power, such as a weak stator, missing on one cylinder, plugs, etc. A good mechanic will be able to determine the problem.