Wow, thanks for all the info guys! I can see a clear pattern with only a few conflicting ideas. I am going to try most of them this week. I unwillingly took a break last Friday and my legs are feeling stronger today than they have in weeks.
However, I'm going to slow down, up my cadence, start stretching, and try to slowly push my miles up past my commuting distance. Water and nutrition are a big focus but I can improve there too. Thanks to everyone who took the time to help!