Thanks for all of the suggestions. I had to work 24 hours on Saturday, so I was planning on coming home Sunday morning and getting straight to work. Apparently my parents and girlfriend had worked on the pool all day on Saturday (I think they're ready to go swimming). This is what I came home to.
Wow, they did a lot of work. They actually went out and bought a submersible pump to use (they plan on using it later in the year to transfer water around to and from rain barrels). They said that the whole time it was draining, they scrubbed the walls and "stirred" it so that the pump would get as much sludge out as possible. So Sunday we worked on the rest. Got all of the water and sludge out of there. We decided to go ahead and completely empty the pool because there were a few low spots, the side furthest away from the return and skimmer was about 2 to 3 inches lower than the side of the skimmer, so we added some sand and did a quick re-level of the pool.
After we got it all clean and ready to start refilling, we found some troubling spots.
These spots are in a 4 square foot area or so. I'm assuming this was caused by the previous owner just dumping in chemicals? I'm not sure, but my assumption is, that the only way to fix such a large area, would be to buy a new pool liner. Any ideas there? Should I be concerned at this point? It's on the bottom, so there shouldn't be too much stress on this area. You can sort of see the area in question in the next photo.
Anyways, the pool is all clean and refilling as we speak. I'm refilling from the well and have the water just barely turned on, so it's just above a trickle of water. Slow enough that I don't have to worry about running the well dry.
Thanks again to everyone that has gotten me this far. Can't wait to get it full (probably about a week or so, filling at this rate) and get all the levels right!