Welcome to the MasterCraft family. Nice looking boat! Hope you make many good memories with it.
1) There is no right or wrong way to mount the pumps . . . but there is a best way! That is, impeller down so that any leaks don't drip into the motor. Simple to just unscrew the pump, unscrew and rotate the pump head (or reverse the switch on the dash,) and remount.
2) Might as well replace the other impellers -- your flow rate will improve.
3) Maybe what you are meaning is that owners replace the hard tanks with bags that can be filled with more weight and also give more storage space when empty. I think most people use rear ballast (one side or the other or both) most of the time, depending on whether its boarding or surfing.
4) Yes. In fact, I'll be installing a integrated bow sac tomorrow which fills from the KGB. Got it from wakemakers.com
2005 X2, Viper Red, MCX, OJ TZ-X5 prop, PPass, rear 750 sacs, KBS, IBS, Bennett Wake Plate, custom wake shaper
(previous) 2001 X5, 1991 TriStar 190