Simple Clicks per second Game

A) What is the best method to use as a timer

The millis() function. Record when loop() starts, if that hasn't been recorded before.

B) What is the best input function to use in the code

To get what? The switch press? That would be digitalRead(). Keep in mind that it is not that the switch is pressed that is important, as much as it is that the switch is now pressed but wasn't before. This means that you need to keep track of the current and previous states.

C) Will A + B interfere with each other

No.