Four weeks, and a lot of work, in and the house is feeling much more livable. No more leaky toilets. All four bathrooms are fully functional. The red water turned out to be a normal thing for an older house that has been vacant and, thanks to advice from my dad, it was fixed by 20 minutes of running water and zero dollars.
The not so good news is that our master bedroom ceiling has tested positive for asbestos and the hallway is going to need to be tested for lead before we can paint it. Looking on the bright side, we should end up with scraped ceilings in our master without spending the time and energy to do it ourselves.