We have not processed T2-weighted images much -- the people we work with at the NIH don't use them very often.
How are you evaluating the uniform-ization? By histogram?
One option would be to use 3dUnifize on a T1 volume, and save the scale factor with the '-ssave' option, then apply that scale factor to the T2 volume.
Another option would be to send me a T2 volume, plus a description of how you are judging the quality of the result, and then I can mess with 3dUnifize to see if it can be beaten into doing something more usable.