I just didnt see a Place Diverter in your list of goodies thats why i was asking.
I'm not sure who's impeller you have in your pump or what an A-1 is, but with Berk and AT impellers an A is pretty aggressive and you should need alot more power to pull the rpms up to 5800 RPM. The leak by the shaft could just be that you need to tighten up your packing seals, you dont want them too tight though. They should slowly drip water at an idle to help cool/lub the seals and shaft. It's possible that maybe your pump needs a rebuild. Somthing doesnt sound right to me, you should be able to run faster than 58 MPH with 500 HP.
Like i said, with my old 500ish HP deal, with a MPD loader, AT Droop, Place Diverter, and old worn berk A impeller the boat ran 86 MPH... Oh and i was spinning the 5500 RPM.
Do you have any video or pictures of the boat on a WOT pass? would be interesting to see how much boat is in the water.
Oh and BTW, My new motor which is pushing 670 HP with a new stainless AT A impeller i'm currently only spining 5400 RPM and the boat is running in the low 90's now.
Gets some pics up! Oh and Welcome to the boards!