Engine Computer and Ballast Tanks - 2 Que

I recently purchased a 1999 Super Sport and have two questions:

Question 1: When I open the throttle all the way (was testing the top speed while the boat is still under warranty), after the RPMs get to about 5,000, the motor skips as if not enough fuel is getting to the engine (like a clogged fuel filter). The marina where I bought the boat says that this happens because the boat's engine computer is not programmed to handle process over 4,500 RPMs. Does this sound right?

Question 2: The ballast tanks take about 15 minutes to fill (going at more than 20mph) and more than an hour to empty (while standing still). Using the "fill/empty" switch does not seem to speed up the process at all. Is this normal? Any reccomendations?

Thanks!!!

For question 2, how long should it take to fill/empty if I do what you say? Should I use the fill/empty switch? My manual says that running the boat with the valves open fills the tanks, I am confused? Also, is the fill/empty switch associated with one of the acc buttons on the circuit breaker?

Thanks again!!