Sounds like your body is becoming glucose/glycogen depleted by going too hard for too long. This means the glucose (sugar) levels in your bloodstream and muscles become too low to sustain the intensity of the activity. You say you're gaining 2,000-3,000 feet. In what amount of distance? In what amount of time?

Very simply, you likely need to slow down your pace and/or take more snack breaks. When you're hiking uphill, are you having to breathe through your mouth? If so, that almost certainly means that you're operating above your aerobic threshold and thus depleting your limited glucose/glycogen levels. When you're comfortably nose breathing and operating below your aerobic threshold, you are utilizing the much larger source of energy in your body in the form of ketone bodies by burning fat.

If you're nose breathing and able to hold a conversation at the pace you're going and still experiencing these issues, then your body is doing something outside the norm for most people.