I've put off dealing with it a few weeks now, but the time's come... Tomorrow, I'm going to take the toilet out and rip the tiles up from the floor to see just how bad it is. I'm hoping to finish up all the work over the weekend, but we'll see... I have no idea how much work will be involved or how long it's going to take.
At least the house has two bathrooms, one in my bedroom and one in the hall just outside my bedroom. I can pull things apart in the master one for as long as I need and still be able to have a functional house. :)