How would i keep a Gui invisible for a certain amount of time?

I think the whole script could be cleaned up.

First. You will never get your Shop back if you assign your gui's visiblility property as false

game.StarterGui.GunShopGui.Box.Visible = false
game.starterGui.GunShopGui.OpenAndClose.Visible = false
--The rest of the script
game.StarterGui.GunShopGui.Box.Visible = true
game.starterGui.GunShopGui.OpenAndClose.Visible = true

Second. You are making the changes above on theStarterGui, or in a "GuiStorage", as I call it. So you will only get the results once you respawn you character. To prevent this, you can use the script.Parent technique as you did on the intro. Assuming the intro is like script.Parent.Parent.Parent inside the StarterGui (if not, correct by yourself)

script.Parent.Parent.Parent.GunShopGui.Box.Visible = false
script.Parent.Parent.Parent.GunShopGui.OpenAndClose.Visible = false
--The rest of the script
script.Parent.Parent.Parent.GunShopGui.Box.Visible = true
script.Parent.Parent.Parent.GunShopGui.OpenAndClose.Visible = true

And finally, you can make the transparency system look more fluid. Instead of writing lots and lots of lines, you can just use a while or a for loop:

INSTEAD OF:

script.Parent.Transparency = 0.05
wait(0.05)
script.Parent.Transparency = 0.10
wait(0.05)
script.Parent.Transparency = 0.15
wait(0.05)
script.Parent.Transparency = 0.20
wait(0.05)
script.Parent.Transparency = 0.25
wait(0.05)
script.Parent.Transparency = 0.30
wait(0.05)
script.Parent.Transparency = 0.35
wait(0.05)
script.Parent.Transparency = 0.40
wait(0.05)
script.Parent.Transparency = 0.45
wait(0.05)
script.Parent.Transparency = 0.50
wait(0.05)
script.Parent.Transparency = 0.55
wait(0.05)
script.Parent.Transparency = 0.60
wait(0.05)
script.Parent.Transparency = 0.65
wait(0.05)
script.Parent.Transparency = 0.70
wait(0.05)
script.Parent.Transparency = 0.75
wait(0.05)
script.Parent.Transparency = 0.80
wait(0.05)
script.Parent.Transparency = 0.85
wait(0.05)
script.Parent.Transparency = 0.90
wait(0.05)
script.Parent.Transparency = 0.95
wait(0.05)
script.Parent.Transparency = 1.00
wait(.1)
script.Parent.Parent.Music:Stop()
wait(.1)

Use this:

while script.Parent.Transparency < 1 do --while the label's transparency value is lower than 1, or else, while you can see the label
script.Parent.Transparency = script.Parent.Transparency + 0.05 -- add some transpareny to the label
wait() --fluid process and crash prevent
end
wait(.1)
script.Parent.Parent.Music:Stop()
wait(.1)

Or this:

for i = 1,20 do -- because 0.05*20 = 1
script.Parent.Transparency = script.Parent.Transparency + 0.05 -- add some transpareny to the label
wait() --fluid process
end
wait(.1)
script.Parent.Parent.Music:Stop()
wait(.1)

And what about this loading lines? Can't we do the same? Obviously we can.

INSTEAD OF

script.Parent.Text = "[ 5% ]"
wait(0.15)
script.Parent.Text = "[ 7% ]"
wait(0.15)
script.Parent.Text = "[ 9% ]"
wait(0.15)
script.Parent.Text = "[ 20% ]"
wait(0.15)
script.Parent.Text = "[ 35% ]"
wait(0.15)
script.Parent.Text = "[ 34% ]"
wait(0.15)
script.Parent.Text = "[ 35% ]"
wait(0.15)
script.Parent.Text = "[ 35% ]"
wait(0.15)
script.Parent.Text = "[ 35% ]"
wait(0.15)
script.Parent.Text = "[ 35% ]"
wait(0.15)
script.Parent.Text = "[ 35% ]"
wait(0.15)
script.Parent.Text = "[ 60% ]"
wait(0.15)
script.Parent.Text = "[ 60% ]"
wait(0.15)
script.Parent.Text = "[ 74% ]"
wait(0.15)
script.Parent.Text = "[ 83% ]"
wait(0.15)
script.Parent.Text = "[ 83% ]"
wait(0.15)
script.Parent.Text = "[ 83% ]"
wait(0.15)
script.Parent.Text = "[ 97% ]"
wait(1)
script.Parent.Text = "[ 100% ]"

Use in pairs function

local l = {5, 7, 9, 20, 35, 34, 35, 35, 35, 35, 35, 60, 60, 74, 83, 83, 83, 97, 100}

for i,v in pairs(l) do
script.Parent.Text = "[ "..v.."% ]"
wait (0.15)
end

Whole script

local l = {5, 7, 9, 20, 35, 34, 35, 35, 35, 35, 35, 60, 60, 74, 83, 83, 83, 97, 100}
script.Parent.Parent.Parent.GunShopGui.Box.Visible = false
script.Parent.Parent.Parent.GunShopGui.OpenAndClose.Visible = false

wait(1)
script.Parent.Visible = true
script.Parent.Parent.Music:Play()
script.Parent.Text = "[ Loading ]"
wait(1)

-- the in pairs loop
for i,v in pairs(l) do
script.Parent.Text = "[ "..v.."% ]"
wait (0.15)
end

--loop 1 (choose one)

while script.Parent.Transparency < 1 do --while the label's transparency value is lower than 1, or else, while you can see the label
script.Parent.Transparency = script.Parent.Transparency + 0.05 -- add some transpareny to the label
wait() --fluid process and crash prevent
end

--loop 2 (choose one)

for i = 1,20 do -- because 0.05*20 = 1
script.Parent.Transparency = script.Parent.Transparency + 0.05 -- add some transpareny to the label
wait() --fluid process
end

wait(.1)
script.Parent.Parent.Music:Stop()
wait(.1)
script.Parent.Parent.Parent.GunShopGui.Box.Visible = true
script.Parent.Parent.Parent.GunShopGui.OpenAndClose.Visible = true

Do you see? If you try to learn something more, you can reduce your script lines!! In this case, the lines were reduced in more than 50% !!!