It sounds like there may need to be some changes in some of the core things you do fundamentally. What are you doing for stretching, nutrition, hydrating, etc…? You clearly have a good base, but can you build a better one? I would take a step back and evaluate how you have been doing things and adjust one or two of these things. For example, are stretching dynamically before every run? Are you stretching statically after? Are you eating after every run?
After evaluating the fundamentals, I would design a training that would allow you to be strong in the end. This means lots of threshold training and speed play. Do train on hills often? Adding more hills may give you strength. Adding hills into the end of your long run could help.