I installed 3/4" hardwood planks over 3/4" plywood (16" wide, kerfed every 12", with 1/4" expansion gap) on top of concrete slab.

So the floor went up about 1.5" everywhere. There is a bathroom which is still sitting 1.5" lower, that I want to bring close to the hardwood floor level, and re-do with vinyl tiles.

In that bathroom, I'm planning on nailing two layers 3/4" ply at 90 deg to each other. Bottom layer 16" wide, kerfed every 12" with 1/4" gaps just like for the hardwood subfloor. Top layer no gaps in between the sheets but 1/4" all around the periphery; no kerfing. Top nail with a 34 deg angled nailer (every 9"?). Then install the vinyl tiles.

1. Does all this sound OK?

2. The toilet bowl will be 1.5" higher than the flange. How do I fix that huge space, do I just stack a few extra thick wax seals on top of each other? Or do I need to install a connecting tube or something? Or should I just call in a plumber? I did the upstairs toilets myself, but there was no height diff there (no concrete, so no extra 3/4" ply, and I left the bath floor slightly lower than the hardwood).

You need to call a plumber to add an extension on the pipe. Mulitple wax rings are not a good idea around wood.