I recently woke up with an inner ear ache. and my jaw is sore. with a headache. what could be the cause?

Ear/jaw joint/teeth: I don't believe what i call the inner ear has any pain fibers; but the middle ear & ear drum is wired to the same nerves that supply the jaw & teeth. Pressure on / in the ear drum from infection, jaw or jaw joint & dental pain may all give pain thar radiates to the ear on the same side. If it is simple jaw joint pain (biting a popcorn kernal wrong) Ibuprofen might help but an exam might be needed.

Grinding/ Clenching?: If you are clenching and/or grinding your teeth at night, you are likely to wake up with jaw pain, ear ache, headache or s combination. You may also have tenderness over the jaw joint or temple area. Check with your primary doctor or your dentist to verify.