Howdy. Nice boat ya got there
... got pics?
Anyhow, I recently upgraded my ballast to a 750lb Fly High bag in each locker, kept the factory KGB (which is still in really good shape), and added a Fly High 650lb [max] Integrated Bow Sac (IBS) under the front seats. I also replaced my port ballast pump as I think it became a victim of being mounted "upside down". So, to answer your questions...
1. I bought a new Jabsco Ballast Puppy to replace the port pump which was weak. I swung the pump head around 180 degrees so I could mount the new pump unit pump-head down though, which should keep it dry and make it live longer.
2. The 750lb bags in the rear lockers fit well. You don't have to fill them all the way for wakeboarding if you don't want, but you have the option to for surfing. Pretty flexible setup.
3. Take them out. The 750s won't fit with the hard tanks in, and you gain a bunch of storage space by taking the hard tanks out (when the 750s are empty, at least). Also, the plumbing is a bit simpler on a single bag, rather than a tank/bag combo.
4. See above
Also, you'll want to upgrade the impellers in all your [Jabsco] ballast pumps to the green ones. In fact, that could be the reason your KGB and starboard ballast aren't filling/draining well.
Take a look at www.wakemakers.com
for all the gear you're looking for. Check out their "tankbuster" kit for the rear lockers - comes with all the parts you need, and you get a good selection of bag sizes. I found their service beyond excellent. Give them a call, I'm sure they'll set you up with exactly what you're looking for... including something that will fit in the factory KGB location.
Hope this helps...