Body aches/muscle aches are common with viral illnesses. The body aches will subside when the viral illness begins to go away. This will sometimes take upwards of a week. If you are having flu-like symptoms (especially with body aches) chances are you have influenza. Diarrhea is a common component of Influenza. You can continue to take the Tylenol and some Immodium for the diarrhea (loose stools). If you are not better within a week or you begin to feel worse, by all means, go ahead and see your Dr for evaluation.
You get influenza from touching surfaces that other people have touched that have the virus and then you inadvertently rub your nose or eyes and the virus enters your mucus membranes. Influenza is also contracted through breathing tiny droplets in the air from where someone has coughed or sneezed that is infected with the virus.
The possibilty remains that you are concentrating more on the aches when you are lying down at night because you are trying to go to sleep. Also, body aches seem to worse at night because the body temperature naturally rises at night. Try taking 2 extra strength Tylenol about 45 minutes before you plan on lying down (this will help the body aches). While I can't say it is 100% normal because I don't know exactly what is wrong with you as I can only speculate here on the internet, but from what you are telling me, it sounds like Influenza and the body aches are very common....especially at night when you are lying down trying to sleep.