I had a pretty good kick in HS-a few things that I think helped me:
Almost always finished off a workout with the last rep significantly faster than the average. At the very least, get used to increasing speed of every rep of every workout.
Fairly often, my coach would throw in an all-out surprise 200 at the end of workouts with very little rest after the "last" rep of the workout. That helped with getting used to running fast when tired.
On the same note, be used to running fast. If you want to be able to run your normal 3k pace and then switch gears, you gotta practice that higher-end speed in workouts somehow. Strides after workouts, or just the above two tips. Whatever works.
Maybe consider adding in plyometruc work after workouts a couple times a week if time permits.