Body aches every night for 3 days after swimming along with week long headache, upper back muscle pain, had a ct done for amoeba but doc said brain ok?

Pain after swimming: If you are doing rotary breathing, you may be pinching a nerve at the base of the skull that supplies 1 side of the head, up to the ear and sends a brance down into the shoulder ending on the inside of the ptip of the scapula. Try not swimming or doing rotary breathing for a few weeks and see if this pain resolvs.

Complicated: Amoebic encephalitis would have manifested itself in a more aggressive fashion by now. Sounds as if you might simply have a viral illness, and just because you were swimming at about the same time does not necessarily mean the two things were associated. You need more history and exam than a ct. Hope you are better soon.