What could cause me to wake up with a clogged ear? it's still clogged days later. what do i do?

Common issue: People occasionally have an accumulation of middle ear fluid if it does not drain down their Eustachian tube during a cold, allergies, etc. This can produce a muffled decrease in hearing on that side. You could also accumulate canal wax that might have similar features. Your regular doc could examine you if this persists & see if treatment is needed.