Although the original question concerned how to pause the execution of the program, might I suggest a different approach to accomplish your objective. Assuming that your code works, except for delays, you might want to set the CSS on your hexagons (either visibility or display) so that they can't be seen when they're drawn. Draw them all, even though the user can't see them, and then use a procedure like I've shown you to make them visible at intervals. That way you wouldn't really have to modify your existing code to any great extent.
Just a thought, and I'm glad if I was of some help to you.