When I test game, the animation countdown of the number 3 is already well into its scale animation before appearing on screen. Is that just my computer being slower than the _ready function? What might be an appropriate way to delay it an extra second? Add a fourth second to the animation itself and just hold on 3 for an extra second?
My other timing question is at the end of the game. Why might the time remaining stop at 00:01 when time runs out? Shouldn't it be 00:00?
It sounds like your computer takes a long time to display the game window, so the timer starts running before displaying the game window.
You shouldn't worry too much about this right now because in a complete game, you would wait for player input before starting gameplay animations. You definitely wouldn't want to add a one-second delay to every player.
If you want to be able to see the full animation on your computer for learning purposes, then yes, adding a delay at the start of the animation is fine and is probably the easiest option.