Have you put a level on the floor? Is it level? Is the floor flat with no humps or dips? Your floor can be a little out of level and still be good to tile on. Being flat is very important though.
I understand the desire to maintain your height, however the 24" on center is kinda pushing the envelope for a safe sub-floor with only the 3/4" ply and traditional setting methods (backer boards). You need to strengthen the floor to keep the tile from coming loose later on. The self leveler does nothing to strengthen the the subfloor. One way to do that is by adding a second layer of plywood, 3/8" would be minimum. You could then install Ditra from Schluter on top of this floor and you would be about a 1/2" above the subfloor. Another option is you could use 1/4" backer instead of the Ditra. Another option would be to go with the Ditra XL. According to the
Installation pdf, Ditra XL is approved for flooring on 3/4" plywood with trusses that are 24" on center. Starting on page 4, it talks about Ditra XL and the testing to use it on 24" on center with tile. On page 5 is the detailed drawing titled, D-W24-XL-T-08. The best part about the Ditra XL, it will raise you about 5/16" above the subfloor plus the thickness of your tile and thinset.
This would be almost like setting your tile directly on you vinyl covered subfloor, which you should not do no matter what. However, you will get an idea of finish height by simply laying the tile on you present floor. As far as the toilet and the height, you can buy longer bolts, longer supply lines, and thicker wax rings to get it back in place and running.