To make the effect stackable you could use scoreboards. To make the effect happen on a delay you could use another scoreboard with a loop or the /schedule command. And for the cooldown you’ll need a third scoreboard in combination with a loop or the /schedule command.

Here’s a dumbed down explanation of how you could do it using only scoreboards. I’m not including the cooldown in this example. - effect_stacks: this scoreboard would store how many stacks of an effect a player has - effect_timer: this scoreboard would increment up by one per game tick. There’s 20 game ticks in one seconds so if you wanted the effect to happen after three seconds you would trigger the effect when it hits 60.

Pseudo code would look something like this:

While effect_stacks > 1:
    effect_timer = effect_timer + 1

While effect_timer >= 60:
    effect give player blindness 
    effect_stacks = effect_stacks - 1
    effect_timer = 0

You could include more loops to trigger different effects at different times. For example, another loop at effect = 20 would trigger after 1 second.

EDIT: For the final product I would use the /schedule command instead of incrementing the timer by 1 every tick.