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I have a pair of these engines on my Outrage 18, so am familiar with the engine. Mercury has NEVER manufactured an engine bracket using blind holes. That was a (terrible) OMC invention, used by them only, and maybe copied by Yamaha? I can see the lower bolts in your installation.

The propeller is the earlier version of a Mercury Laser II without the changeable vent plugs, a Quicksilver "Lightspeed". They are good, fast props. Because of the large stamped numbers, yours is less than ten years old. Although this prop can work on your rig, a 20" pitch version could be more appropriate.

Your problem is that your speed vs RPM numbers do not calculate, as long as your engine gears (2.33) are original and the propeller hub is not slipping. With a given propeller, RPM and speed tend to be a fairly constant relationship. The 5200 RPM max sounds about right with that prop, but the boat should be doing about 42-44 mph. So your GPS reading could be wrong, or your RPM is reading wrong, or the prop is slipping badly. That is where I would begin. A 20" Laser II prop should give your 5500 RPM and the same 42-44 MPH. Because of bottom paint, yours may be closer to 42. The Merc 90 you have is a strong engine, running correctly, close to 100HP at the prop.

The engine should definitely be raised up to the 3rd set of mounting holes. With ANY engine, Boston Whaler recommends on the Montauk for the engine to be mounted in the second bracket hole. In addition, your engine has a longer (taller) than normal mid section length, so it should be up even higher. And the Lightspeed/Laser II is
a "surfacing" prop, requiring a higher engine mounting. If speed is your main objective, you could even install the engine in the 4th set of holes, but for all around use I would stay with the 3rd. Incidentally, your bottom bolts are installed in the wrong direction. Per Mercury's instructions, the lower bolts should have the heads on the outside, indicating your engine installation was not done by the factory, but probably by a Dealership.

I would also get rid of that badly corroded water separating fuel filter. They are not needed in a boat with on-deck fuel tank.

So what I would do is to first get the engine raised up, and check the propeller hub, particularly the black drive sleeve. If good, the engine hub assembly should easily go in and out. Look for 5000 RPM and 42 MPH. If not, check RPM and GPS for accuracy. i am suspecting your tach reading. But if so, than the engine is not putting out the proper power and may need work. Once you get everything running correctly, then change to a lower pitch prop. I think the factory supplied a 21" aluminum prop on your rig, and they are only about $100, but not quite as fast as the Laser II. You should be able to find a good used Laser II 20" on Ebay.