Hi Vinny,
I did look at your data, and I had thought I had answered already - sorry, I think the check got lost in the mail or the browser. Briefly, neither the alignment nor the skull stripping method will work well with the impulse response data that this seems to be. There is not enough structure in the data, and the structure that is there will vary depending on the specific stimulus and experiment. Instead do the alignment and skull stripping using the raw EPI data.
Also, we should probably start posting in new threads to avoid confusion.