I have no idea how you got it to work doing that!! It makes no sense - how would TTR know to get the files from that folder?
I did what you said and it did nothing, so i followed these steps:
> Download the required files using the above link
> Right click the downloaded file and extract it
> Unarchive the extracted file with StuffIt (i'm on a mac) which will leave you with a folder called GuitarHero.app.rar
> Copy the contents of that folder (using SSH) to /Applications/TTR
(NOTE - you might like to copy the contents of your TTR folder for backup.)
> Restart your ipod.