Car is running great, but the CEL did not disappear. I disconnected the negative battery terminal for 3 hours, hooked it back up and the light is still there. Does the code have to be cleared some other way?

 

Read the ECU sticky on the CEL light - there are instructions on how to reset it.

 

With the battery disconnected for 3 hours it should have cleared.... but try doing it manually. You really shouldn't do it by unplugging the battery anyways, because then it resets all of the fuel maps and everything.