Hi and thanks for the query.
This does sound like the acid reflux is complicating things. Constant trickling of acid up the esophagus causes recurrent throat inflammation, pharyngitis and lower respiratory tract infections. Taking Omeprazole decreases the production of acid but does not stop the acid from trickling up and causing irritation. The green colored mucus and the thick phlegm are pathognomic features of acid reflux.
I would suggest the following:
Sleep with a head up tilt of about 30-45 degrees at night. Use a wedge pillow for this purpose.
Refrain from eating barbecued, smoked, salted and spicy foods especially at night.
Avoid alcohol, smoking.
Avoid hot beverages and fizzy drinks especially at night.
Do not eat to a full stomach at one point in time, eat more frequently in smaller portions if required.
A walk for about 15 to 20 minutes before bed time.
Start using an OTC ant acid before dinner.
Ask your PCP for a referral to a Gastroenterologist for a thorough evaluation and possibly an Upper GI endoscopy to rule out any mucosal changes due to the constant acid reflux and to see if there is any lump in the throat.