Your problems are minor, Ed, the solutions rather easy, so relax and enjoy the project.
Welcome aboard, by the way, you done good starting you own thread, just stay with it throughout the project so we can all keep up with what's going on.
Are you sure you have two and a half inch PVC pipe coming up for your drain? Those pipes are sized by inside diameter, a two inch pipe being about two and three eighths outside diameter. That what you got? If so, the standard Oatey drain will slide right on. Two and a half inch PVC isn't common unless it's grey in color, which means you have the electrical service conduit stubbed up in your shower.
As for the floor hole, just get the pipe the way you want it, then cut a couple pieces of 2x4 or strips of your 3/4 ply a little longer than the side of the hole (either direction, whichever is easiest), slide them down into the hole, hold them up against the bottom of the floor and screw them in place through the floor from the top, using holes you have pre-drilled. Then cut a piece of 3/4 ply the size and shape of the hole (needn't be all that accurate) with a hole in the middle for the drain pipe and screw that onto the cleats you have provided. If you've already installed the drain, just cut the patch in half and install the two pieces around the pipe. This all takes a little less time to do than to 'splain.
For the blocking in the walls for the pan liner, do the best you can. Frequently in the plumbing walls you can use some 3/4 plywood for the blocking in front of the pipes. Again, you might cut some cleats to nail against the sides of the studs to allow you to nail or screw the thinner blocking from the front. None of this has to be furniture quality construction, just a reasonably flat place to support the pan liner. If it looks really ugly, don't take no picher until the pan is installed.
