harri – I could be wrong but my understanding was that while nusach sefard is based on additions from suggestions of the Ari, the nusach itself was actually formulated quite a while after he lived.
With the exception of Musaf on Yom Kippur which he davened Ashkenaz, all the other tefilot of the year I believe he davened Sefardi (i.e. Edut Mizrach) and explained his kavanot according to that nusach. My teacher told me two possible explanations of this – some say that the Ari held that the Sefardi nusach was actually more correct, and others say that since the main reason his neshama came into this world was to teach Torah to Rav Chaim Vital (who was Sefardi) he taught according to Rav Vital’s nusach.