Running temperature, headaches come and go, could a kidney infection cause this, was having problems by not drinking enough water, now I drink 2 to 3 bottles a day, kidney has gotten better, but still running a slight fever about 99.5.

Fever. Fever is 100.5 and above and is a sign your body is working, fighting an infection viral or bacterial. Treat symptoms if you need to, otherwise keep drinking at least half your body weight in ounces avoiding all caffeine. Hope this helps.
That . That is a low grade fever and not concerning. Call your doctor if your fever is over 101 degrees f. Yes, it is possible that you are experiencing a low grade fever due to the kidney infection you had. Your body may be rehydrated, but your immune system is still fighting. You seem to be doing well. Call your doctor if your fever is higher than 101 degrees f.