LINE 3 invalid argument #2 (string expected, got Instance)?

the value is a string value

script.Parent.OnServerEvent:Connect(function(player, Item, StorageSlot)
	local SlotToStore = StorageSlot
	if player.SafeStats[SlotToStore].Value == "Empty" then

		player.SafeStats[SlotToStore].Value = Item
		
		
		if player.Backpack:FindFirstChild(Item):FindFirstChild("Clips") then
			player.SafeStats[SlotToStore].SS.Value = player.Backpack:FindFirstChild(Item):FindFirstChild("Clips").Value
		end
		
		player.Backpack:FindFirstChild(Item):Destroy()
		script.Parent.Parent.Parent:Remove()
	end
end)

You're probably comparing a StringValue named Value to a string, try adding the Value property.

script.Parent.OnServerEvent:Connect(function(player, Item, StorageSlot)
    local SlotToStore = StorageSlot
    if player.SafeStats[SlotToStore].Value.Value == "Empty" --[[Better!]] then

        player.SafeStats[SlotToStore].Value.Value = Item


        if player.Backpack:FindFirstChild(Item):FindFirstChild("Clips") then
            player.SafeStats[SlotToStore].SS.Value = player.Backpack:FindFirstChild(Item):FindFirstChild("Clips").Value
        end

        player.Backpack:FindFirstChild(Item):Destroy()
        script.Parent.Parent.Parent:Remove() --Remove is deprecated, try using alternatives such as .Parent = nil or :Destroy()
    end
end)