I'm waking up in the morning coughing dark brown mucus my throat hurts and my ears do sometimes as well. i am a non smoker. ?

Bacterial infection: Dark brown mucous could be dried blood. I know this may sound scary but I'm guessing you've been coughing a lot and really hard. Its easy to rupture capillaries or alveoli since that are so very thin. Capillaries are one cell thick and alveoli 2μm-600 nm. The throat and ears suggest a sinus infection. Its best if you see your primary care doctor.