Okay, so here is what I have done:
I started by cleaning the area where the leak started first. my toilet is in a separate room from the shower, and the shower room + bathroom room can be closed off with a door on either both sides. (basically a large bathroom with a sectioned off toilet).
I took a bleach + detergent cleaner, 50 parts bleach, 40 parts detergent, 10 parts water. I understood that bleach released spores, but it kills the area the spores were resting in. The detergent helps keep the area clean and helps the bleach solution stick to not let mold grow back. I researched this heavily before selecting this option, and it was the best option for me at the time.
I wore a $40 respirator (with two filters on the mask) from Lowe's, rubber gloves and sealed eye protection. I didn't find a full suit unfortunately.
The bathroom is linoleum, and I checked the area where the leak was and there was no damage underneath, which was good. It appeared to be stopped since the linoleum was bent upwards, and funneled it to the carpet. I scrubbed every inch of the floor, walls, toilers, cabinets, shelves, sink, shower, ceiling, etc. You name it. After I was done, it felt clean in there, and the girlfriend could breath.
She is still having some difficulty, so I bet I hit the source real good, now I just need to hit the army! Will be ripping out the carpet tomorrow to check underneath. Will check padding and any insulation there.
NOTE: When the issue first happened, I took every measure to dry the wetness. All windows open, GF put a blow dryer down on the carpet to stipend the wetness, and we laid many a towel to keep it dry. Plenty of air flow, but it was wintery so it was probably not effective. This was all we were able to accomplish, but now major changes need to be made.
We turned off the humidifier tonight and clogged the top with a pillow. Will leave it this way for a few days and see how it goes.