The Water Goes Down the Hole

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Last week, I noticed that the floor was a little squishy in our bathroom downstairs. If you stepped on the cracks between the linoleum tiles (quiet you in the peanut gallery, we don't really like them either) your socks would get a little wet. Toilet 1, Scot 0. With everything going on, I decided that it would be fine for a week. So, having completed my dissertation defense, I now had some time. I kind of wish I didn't. At least it should be about a 1 hour, $10 fix. Meaning 3 hours and more money, since it's a DIY project.
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First, I don't like plumbing. It makes me swear (ok, usually just under my breath). You always have to get into weird positions and there never seems space to turn the wrench right, you always bang your knuckles on something, water always gets everywhere (in this case, toilet water), etc. I looked up a DIY site to find out what the problem could be and guessed that the wax seal had given up the ghost.
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I've replaced components in the toilet tank and even the seal between the bowl and tank, but hadn't ever seated a toilet. My dad has done it a couple of times, so I asked him for some advice. It was mostly the same as I read and to lift with my legs (I think her threw out his back once).
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The nuts holding the base to the floor were rusted to the bolts, of course. I got one loose enough to fit a hacksaw blade between the toilet and the nut and after 30 minutes of 1" saw action back and forth, pried the nut off. I wasn't going to do that for the second nut and bolt that were closer to the wall because of impossible angles and the general laws of physics, so I ingeniously thought of the bottle of WD-40 in the closet. I sprayed the nut and bolt, waited a few minutes, jammed a screwdriver between the nut and toilet (so the bolt wouldn't turn), and viola! The nut came right off. I love you WD-40.
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After getting the toilet up, I scraped off all the old wax and put the new wax ring in place. I seated the toilet bowl, attached the tank, reattached the water, caulked around the base of the toilet and was generally happy with my work. I noticed that before, some water went under the framing in the hot water heater closet, so I used my shop vac and cleaned it up. Toilet 1, Scot 1.
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After doing a few other projects (caulking in a bathtub because I had the caulk gun out, which is always fun), deciding on homeowner's insurance, looking at the home inspection, etc., I went to check up on my work. I noticed that there was MORE water in the cracks and a little further away from the toilet. Toilet 2, Scot 1.
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After practicing my techniques, I had the toilet disassembled in about 5 minutes, this time using the shop vac to suck up the water instead of a sponge and bucket and Becca acting as an assistant to get me tools I needed. The other thing I read was that a leak could be caused by a cracked flange. When I got the toilet off, it seemed like the wax was a little too thin in some areas. I checked out the flange and it was a solid metal piece that was part of the pipe that went into the floor. I dried everything out with a box fan and caulked around the flange. I found an extra large wax ring (40% more!) at Home Depot. I'll call it Toilet 2, Scot 2. I'm waiting for the caulk to dry, but I'm hoping for better results this time.
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Looks like we're heading to overtime. Plumbing, that jerk.