With the amount of hours I would be getting the superchargers looked at and serviced, which could be one of the reasons why the get up and go has started waning. The issue in relation to the revs through is something of an indicator that the wear rings and/or impellers may be damaged or worn and need replacing.
The wear rings and impellers are something that you can usually do yourself with plenty of help and guides on the 'net. The superchargers through, can be done, but are something more mechanical and unless you are that way inclined, would be something you need to take it in for. I think the washers in the 2005 series were metal, but it is something you should get checked, especially if the supercharges have been serviced before. The earlier models had ceramic washers which, if they go, can cause some significant engine damage and lots of $$$$$.
Other than the usual servicing and the like, they are a fantastic boat and you should have a stack of fun with it,
I have a 2005 Speedster 200. The intake grates do not go up high enough to touch the drive shaft. This would actually be counter productive. It is designed to capture anything before it gets into the intake. If it moved up that high, it would expose the intake and be useless in doing its job. If yours does go that high, something is amiss.