I appreciate the suggestion. I am actually going to do something similar. I am going to sister 2x8s alongside the current floor joists and level off that way in order to avoid another mortar bed.That way all the joists are level and I can just lay the 3/4 plywood and that would be level too. I will then spread some thinset attach 1/4 backerboard and then tile on top of that.
After the experience of laying one bed down and then having to rip it out, I am now trying to see if I can just totally avoid needing mortar at all.