I Have A Three Year Old... She's Been Congested And

I have a three year old... she's been congested and has finished 2 rounds of antibiotics the last one was for ear infection... she's been running a 100-101 fever last two days so took her back in to check her ears... they said the ears look fine but her throat is red so they did rapid strep test and said it was negative.... but all day she's on and off crying about her left ear, her throat ,stomach, and also her eyes hurt... I'm at a loss what it could be... there is definitely something wrong