Welcome to Health Care Magic.
Based on the information provided, the throat pain and the recurrent fever
you have been experiencing is due to Pharyngitis
Unless the primary cause( GERD in your case) is treated, you continue to have fever and throat pain.
Treatment of GERD includes using of Proton pump inhibitors ( omeprazole or pantoprazole
) in combination with a prokinetic agent ( Domperidone
or Itopride) .
Along with the above medication , you need to change your dietary habits. You can not eat what ver you want.
Try to restrict fat and spice in your diet. Avoid all kinds of carbonated drinks and Beverages. Do not take hot dairy products especially at nights before going to bed. Try to take small multiple meals instead of heavy meals. Do not go to bed immediately after taking food, just wit for atleast 1 1/2 to 2 hours. You will definitely notice an improvement in your condition.
Betadine or salt water gargling will relieve the throat pain.
Hope you got my point