Consistant headache, sore throat, ear pain, gums hurt, body aches, nauseous, negative for strep throat and the flu taken amoxilin,?

2 separate problems . These 2 problems should be addressed separately. 1. swollen gums - can be a sign that you already have, gum disease or dental abscess. See your dentist. 2. Headache, sinus aches, coughing- seasonal flu is very common viral infection with symptoms you have described. Usually the condition resolves on its own with home care. Drink water, NSAIDs and get a good rest. .
? virus. Probably a viral infection . If so, the amoxicillin will not help at all. Course is 3 to 7 days generally. Your physician is the best person to advise you on this.