Hi I had a sinus infection for two weeks and bad headaches/congestion. That is gone but in the morning when I wake up my throat hurts and there is still mucus being coughed up. What is the cause of this? What should I do? Thanks

Post nasal drip. The cause is the sinus infection that you already had. It is left over from the sinus infection. A decongestant such as sudafed and a second generation antihistamin such as zyrtec (cetirizine) should be able to stop it. Pharmacist can help you or your doctor can give you a prescription.
Sinus drainage . you likely had a blocked sinus filled with pus. It unblocked, relieving the pressure causing the headaches, but is still inflamed and draining. Most sinusitis is viral not bacterial her, but the drainage is quite irritating to the throat.you may try an NSAID to help relieve irritation and a decongestant before bedtime might help produce drainage. Chloraseptic spray or generic is best for throat.
Mucus. This mucus could be residual postnasal drip from residual sinusitis, or it could be part of an upper respiratory tract infection affecting the bronchial tubes. These symptoms should eventually subside but antibiotics may be used if symptoms persist or worsen.