So once you use the restore option, you start to apply manually the patchs from 3.2.2.a to 3.3.5.a (refer to guide for patch links). There's no need to start a repair.
If the batch didn t revert the files maybe watch if you have some wow.exe.bak, launcher.exe.bak and battle.net.dll.bak in your wow folder. If you see them delete wow.exe, launcher.exe, battle.net.dll and remove the .bak from the other files.
If you don't have such files, then it means you read between the lines of the guide, and I can't do anything
As for the repair.exe, try later or tomorrow, servers don't have 100% uptime for what ppl have experienced, also check it's not blocked by your firewall or other stuff.