New construction subfloor unlevel

Pretty simple to fix if you have access from underneath. I would start by adding a couple of 2x4 with screws underneath several of the joists on each side of the problem joist.

Next, cut the joist vertically at the location where the bump is. This will let the joist sag down on top of the 2x4 braces that you added.

Finally add a sister next to the joist that you cut. The simplest thing to do is to use a piece of wood of equivalent size as the existing joist. It is glued onto the existing joist with construction adhesive and then bolted together securely with closely-spaced bolts.

Proper way to install double-layer of subfloor? : don't screw the top layer to the joists. And I think, the screws for the backerboard shouldn't hit the bottom layer.

I can't seam to find any manufacturers coming forth and prescribing what the maximum size void is that you can fill with thinset, under a CBU. This is probably dependent on whose thinset you use.

I'd say: anything over a half inch probably needs special attention (fill and let it set completely before proceeding because it will shrink too much). Anything less, I'd just fill as I layed the board.

Try to insure that any edge of the CBU that's going to be parallel to these gaps, ends up being no where close to them. Avoid it like you're supposed to: the seams of the plywood should not match up with the seams of the CBU.

A few screws into the old subflooring might help get everything level.

This doesn't look so far out-of-wack that you'd need to level it, but here's how:

How to level bathroom plywood subfloor before tiling?