I recently took up the carpeting that was in my bathroom when I moved in. And, until I could afford a sweet redo, was going to put down peel and stick 12x12's. The problem I have now is that there is a 1/8th inch height difference between two of the 3/4 inch plywood subfloor (where they meet).
I would like to prep the floor the right way and make it good for the peel and sticks. Eventually I will probably put down some cement board and tile. I have purchased some self-leveling floor compound and recommended primer from Home Depot.
I had a very similar situation when I bought my place - not with the uneven subfloor, but with needing to replace the bathroom flooring. We chose to do peel & stick as a temporary solution, but it wasn't long before we tore those up and laid tile on hardibacker. The peel & stick tiles were money wasted. My advise is to consider doing your sweet redo piecemeal since you can't afford to do it all now. Consider doing just the floor while living with your current toilet, lavatory, and tub/shower for now. You can replace those elements as money allows. If the difference in price between peel & stick and real tile is too great for now, maybe consider just throwing down the cheapest roll-out vinyl you can find just to protect the subfloor until you can save up a few hundred for the concrete board and tiles.
Sorry I don't have advise for leveling the subfloor, but I thought I'd offer my suggestion based on personal experience.
I agree with doing the tile first if it is in your budget, and waiting on the main fixtures. But if money doesn't allow for that the peel n stick will get you by. The self leveling mix will solve your problem, just make sure your subfloor is very clean-no dust etc before applying, allow time to completely dry ,also dust free before applying peel n stick tiles-very important.