How do I add a click cooldown to this script?

The most common form of cooldown of this type is usually called a debounce, which is actually fairly easy to implement once you learn about it.

local debounce = true
script.Parent.Equipped:connect(function(mouse)
    mouse.Button1Down:connect(function()
        if debounce == true then
            debounce = false
            script.Parent.Input:FireServer('Mouse1', true, mouse.Hit)
            wait(1)--put the cooldown you want here
            debounce = true
        end
    end)
end)

When the script is called, it checks if the debounce is true, if it is then you set the debounce to false, go through with whatever code you want, wait a time, then set it back to true. This makes it so that it can't activate again until debounce is set back to true.