Have you tried already to edit the patcher file so it times out less fast here
as that should be a big help already if your connection is slow.
Another thing you can do is download the manual patches here
After getting your game up to date you dont have to run the game from the patcher but you can just skip directly to grand fantasia.exe in your grand fantasia folder.
Note you do need the latest patches or you wont be able to play as it will say your using a different version.