Hi Jian,
I don't quite understand what you are doing here. What I would do is to recreate the dataset with the proper timing information to reflect how each dataset was acquired. Then run 3dTshift with the same tzero option, forget the -slice option in this case. It looks like you'd want -tzero 0. But think it over yourself.
Lastly, why or why are you using .hdr formatted datasets? Use NIFTI format if you are gong across software platforms!
cheers,
ziad