Hey Dan- Welcome to the forum!
1- You could get rear bags with two drains made, but custom bags are very pricy. You are better off with off-the-shelf 1100s and then installing another drain yourself as outlined above to save yourself a few hundy.
2- You should be able to use your existing switches with a little rewiring. Are you talking about 3 switches each with 2-way rockers (fill / drain)? With 3 bags you are still just doing a fill/drain on each.
3- The little 750 drain pumps are most likely going to have 3/4" lines. You could keep and reuse those to save your budget a little. They can share a thru hull but ideally you may want them individual so you can tell which bag is empty and which is not if all are running. My setup shares a thru hull for the drain and vent (with a one-way valve on the vent line) for each bag - so 3 total. 2 Fill pumps can share a thru hull but they may end up competing with one another when running at the same time (mine do). Would definitely suggest 1" for the fill side. If you have the room and can keep them below where the water line is to ensure good priming you may want to go with individual thu hulls per pump. Sorta depends on your level of patience waiting for bags to fill too.
Then there's always the single reversible pump per bag option - somebody's sure to chime in on that.
4 - I did the battery move a couple season's ago from the rear compartments to up under the glove box. Cabling gets a bit spendy but it is worth it to have full use of the rear compartments for ballast. Plus a necessity if you are going with 1100 bags with drain pump lines connected off the bottom rear at the back of the boat.
1100's will not get quite full in your MobiusV rear compartments (too big of a bag) so you may have to jockey the bags around when filling every once in a while to make sure you get them as full as possible. The 1180 gravity games bag will fit in your basement locker nicely, just a little crowded up in the bow. I'm assuming you have the playpen seating...
Lots of help here on the forum and www.wakemakers.com is definitely your friend.
I went through a very similar upgrade with batteries and ballast, pics always available - and always helpful to post and show what you've got and are working on or asking about.