How do I make the GUI appear and then go away?

I don't think the way you are approaching this is a very efficient way, while server scripts are good for a lot of things, meddling with the player GUI isn't one of those. You should really just use a local script to make it a little easier. The reason being that server scripts can't directly modify the player GUIs. I say directly because server scripts can still give input through remote events, but those aren't necessary for this purpose.

Procedure

To accomplish this in a local script, you have to :

1) Have a touched event to sense if something touched a part

2) Check if the thing that hit the part is a descendant of the character of the local player

3) Move a GUI on the screen

4) wait a given amount of time, then move it off the screen

If you want to have a smooth transition, I'd recommend using tween service or the TweenPosition function of GUI elements.

local player = player.Players.LocalPlayer
local frame = script.Parent
workspace.Part.Touched:Connect(function(hit) -- 1
    if hit:IsDescendentOf(player.Character) then --2
        frame:TweenPosition(UDim2.new(0.3,0,.3,0))--3
        wait(2)--4
        frame:TweenPosition(UDim2.new(1,0,1,0))--4
    end
end)    

you can also change around the aesthetics of the tween by modifying the TweenPositon function:

GUI:TweenPosition(Udim2pos,easingDirection,easingStyle,time,overidable )

Ex: gui:TweenPosition(Udim2.new(0,0,0,0),Enum.EasingDirection.In,Enum.EasingStyle.Sine,2,true)

Use Visible unstead of remove, this is only for text boxes, text buttons, etc.

function touch(hit)
    if game.Players:findFirstChild(hit.Parent.Name) ~= nil then
        local player = game.Players[hit.Parent.Name]
        if player.PlayerGui:findFirstChild("Shop") == nil then
            local gui = script.Shop:clone()
            gui.Parent = player.PlayerGui
            repeat
                wait()
            until (player.Character.Torso.Position - script.Parent.Position).magnitude > 5
            gui.Visible = false
        end
    end
end

script.Parent.Touched:connect(touch)