Ok, so here we have the new hot and cold water pipes, the waste pipe, the thermostat for the heated floor, and the box for the GFCI to connect the heated toilet seat to. I am running 3/4 copper to the bathroom, and will lookinto running a larger diameter pipe from the street and have it split into 3/4 at the junction for the kitchen and bathroom.

When I cut away the old steal pipe for the cold water the black fluid shown below dripped out. I guess it was water once.
After it all got run and mounted (the copper stops just below the floor to be finished later) I used 5/8 plywood to make the wall flush all the way down to the floor in preperation for the cement board. 5/8 is just a bit shy of the thickness of the lathe and plaster. The gap will be filled with mortar.
Originally I used a "new construction" junction box, but it didnt sit right, and since I am not entirely sure how far it needed to protrude from the plywood I replaced it with a single gang version of the one pictured below. It is quite a bit more expensive, but it has 1 1/2 inches of depth adjustment using a screw. It is pretty awesome., I used another for the box for the heated towel rack. The double gang is 4.30 at homedepot.

Progress?

So I have been spending a boat load of time working on the bathroom, but feel like it is still miles away from completion. Here is the last two weeks or so:

Got the walls off a little more, and had to sister the studs under the window. The studs were also cut into to allow for plumbing. You can see the old pipes still in the wall (the big 2" one, and one behind the lathe in the little hole). These pipes are no longer used, and it took some work to get them free. A 24"chain pipe wrench along with a giant regular pipe wrench to get it all free. It ran up to the roof where it vented, but none of it was connected to the stack, so I took it all out.

After we got the pipes out we had to reinforce the studs. You can see where the short studs are cut into again to allow for the waste water pipes, and how I suspended the vent pipe so I can remove it later. I hope I can remove it later.

Here is the room from the door. You can see the part of the subfloor I replaced. The white bucket is covering up the toilet flange so the neighborhood fumes dont fill up my house.
Here is a close up of the replaced subfloor surrounding the toilet flange, and going under the wall into the closet in the next room. Its not very pretty and ideally it would be one solid piece, but since the subfloor ship-lap was 80% removed for plumbing I had to get something in under the bottom plate which meant cutting a smaller piece that would slide in. And by slide, I mean get the shit pounded out of it.
A little better view of the replaced floor. You can see into the next room beyond the stack. Thanks Robert for soldering up the new copper for the toilet.
Looking up from the basement. I added the diagonal support because the one that was there originally was cut in half to make room for the stack. The diagonal piece is just a 2x4 with two 2x4 braces unerneath. All the pieces were toenailed in. (Cheap-o Harbor Freight nail gun, has worked well so far, but dang it is loud. ) I hope this is enough, or a good idea. Since there was nothing there before, I have a hard time believing it will ruin anything.
This is from the closet in the next room. This part of the floor was not rotted, but it was the end of the rotten piece from under the toilet. Had to remove the whole board because what was left after cutting out the bad parts was only a triangle, and barely there.