I am creating a game that uses the wait for key press command frequently, and I have a timer that I want to activate one as well, after a period of time. Is there a way to deactivate the timer when waiting for a key press and restart it after the key press so as not to get an error waiting for two key presses?

You can actually do just that. Disable the timer when before you go to get a keypress and then re-enable it when done. (My first thought was setting and clearing a flag that the timer checks, but that might end up being the same thing.)