I faffed around for about forty minutes installing shims and hitting some parts of the framing with the belt sander, and I managed to get the plywood as close to level as the rest of the house. That is to say it slopes somewhat, but in an identical fashion to the surrounding floor.
I made the plywood panel quite a bit bigger than I needed, so that the hardwood floor which butts up to the tile will overlap the plywood - and be nailed into it. This way, there is (hopefully) no weak point where the tile may crack. The slight issue here was that my sheet of plywood is about an ⅛ of an inch thicker than the surrounding subfloor. I solved this by marking out exactly where the tile will go...
...and trimming off the excess ⅛ with the a straight bit in the router. This is part way through:
The plywood panel was then screwed off to the framing and secured to the masonry pad with concrete anchors. After that it was solid as a rock and flat too. Yipee!