you have two basic options. your timer should run in a threading.Thread, while you have a loop asking for raw_input.
heres a simple proof of concept https://gist.github.com/195eb18e706736d6d020
you could also use the
ui modules. for ui, you would use a textfield's action to check reponses. you would use a Thread to update a timer label. be sure to have a way to abort the thread, such as checking
on_screen inside the Thread.
SceneView might also work, you would draw and check time within draw()...