Nice looking boat, lets see if i can help.
1) Im assuming you are talking ballast? They should all be able to fill / empty at the same time. You might need to just get new pumps. Wakemakers.com has both the oem replacement and a Johnsom pump which fits in. You could try the impeller upgrade. How long is long?
2) For your weight setup this is what i would sugguest. (2) 750 fly high with adaptors to pump into pumps. 560lbs of lead in the nose, unless you trailer then 2 x 350lbs fat sacs in the walkway and on the seats. That is perfect for wakeboarding. If you are just going to surf then dont fill up the 2 on the nose and just do the center and which ever side you surf on.
3) Im pretty sure you have to deal with the same beeping / menu process with the star gazzer. Once your PP is calibrater, its really pretty simple. I have the PP pro and have been offered the star gazzer from a friend but just dont feel the need to upgrade it.
4) Stereo? I just install a pretty nice system in my boat so ask away. Dual Batteries? Are you going to replace the ripped seats?