Been swimming in a highly chlorinated pool this weekend, now I have a headache, my body hurts, And a low fever. Could it be from germs in the pool?

Unlikely. If a swimming pool is "highly chlorinated", there shouldn't be germs to worry about in the water. The germs that tend to get people sick are from the other people sneezing or coughing towards you (through the air, not via the water). Also, surfaces can transmit germs in a place where there are lots of people. Such surfaces include doorknobs, railings, elevator buttons, bathroom items, etc...