That doesn't sound fun! Is your internet connection stable for all other internet activity you do?
Have you tried syncing your Kobo Touch directly via WIFI, without connecting it to you Desktop version? If that works, you'll have all your books on your Kobo to read while you mess around with the Desktop problem. If it doesn't work, have you logged into the kobobooks.com with your browser? There might be a hiccup somewhere in your user account...