My two penneth worth...
Lack of speed endurance. Nothing new to read here, speedwork and some weight work will be the best remedy. Speedwork alongside weights will work wonders.
For the record, alongside my running/climbing, I do a hefty amount of squats (nothing too heavy, maybe 30kg) 4-6 days a week. I am not holding myself up as a pinnacle of running performance, but it's certainly helping me... don't forget the specific core work either...