Thank you for posting the pics!
Well, it's obvious now that someone did some kind of renovations at some point, and I think without a plumber or renovator who knew what the f*ck they were doing or properly licensed. Key point: the wood not being the same holding the shower valve (it's a lighter color i.e newer), and all those pipe couplings with bands - why did they not use fernco fittings (like I said I'm not a plumber but with all those clamps it DOES NOT LOOK RIGHT) - like Smooky said, do a smoke test. I would bet the smoke would come out of those clamps like crazy. I can't tell from the photos either, but it looks like they went from cast to PVC too (hence the clamps) - and the one photo right below the stud in post #12, last pic, shows the cast iron is deteriorating...which means the house was built quite awhile ago. If it's doing it there, it could be the same way thru the whole house. Cast iron is extremely susceptible (sp?) to sewer gases, and if it's showing that kind of corrosion on the outside, I think it's time to re-do the entire house kinda like mystreba said.
Also, where is that pipe going that is behind the board (last pic)? Thats a sewer/vent pipe, but it stops behind the new shower wood board and looks like someone shoved a piece of drywall over the top of it...I'm very suspicious of that pipe...it almost looks like it might have been the old vent pipe, and they never cut it off at the proper point/capped it.
Also, they cut thru that 2x4. We don't know if that is a structural beam or not. Just by doing that, they could have compromised who knows what structurally. Unfortunately, I am not a structural engineer either. But I do know that is NOT correct. You either avoid that, or find a way to double up the beam some how after you go thru it or cut it to keep the original integrity, or shift the load equally to other stronger beams...
The mold you posted in the first picture shows the toilet was leaking for some time around the flange, but I can see rust along the flange area and it looks like someone took some kind of foam to repair it at some point, or it was original to the flange (i.e. Plumbers putty)
Again, I'm not there, so I can't be sure of anything.
In picture #4, there is board sticking a bit out from what I would suspect is the drywall. Do you see the black spot? That could be mold. Is the shower RIGHT behind that board?
As for the pan, um...dunno. Might have to drill a small hole and place a pinhole camera underneath the pan if it's even possible to see if there is a leak.
I just dealt with a home that had a huge brown spot on the ceiling in the garage, and I was sure that was right where the shower was... and I cut that portion out, and there was the shower drain. It leaked slowly over the seal of drain, but enough over time it had done damge to the ceiling in the garage, but because it was in AZ, no mold. Eastern/mid-west have that problem more than we do (mold/mildew). Story short, we redid the entire shower + drain (customer wanted it anyways).
Can you post a picture of the exterior of your shower, and the interior?
If you've figured out what the problem is do let us know anyways.
Since there was obviously a leak at the flange in the past, there is great possibility that nasty water got under the tile, into the backerboard. If the cast iron isn't the source of the stank, then consider pulling up tile.