While the floors were being sanded, I was also putting wood filler in the cracks between the wood pieces. There were several places that had very minor water damage and the boards had pulled apart a little. The wood filler is stain-able and pretty much disappears after the stain is applied.
I bought several different colors of stain and mixed them together to get just the color I wanted. For the next two days Parke and I stained the floors. Finally Johnny put two layers of polyurethane on the floors.
The process took a whole week and was a ton of work, but the floors look amazing now! Here are the photos. The first two photos are how the floors began, then after they were sanded, then stained, and finally after the poly was applied (You might also notice some changes to the kitchen).