Well they say you should learn something new every day! Since I had some time I searched the www and found a transmission manual. Page 91 has the following Note:
"The flanged shafts are installed with Polygonal bearings. The rough running of these bearings when the flanged shafts are not installed does not indicate that the bearings are faulty. The polygonal bearings can be replaced only with the shaft."
I had assumed they were needle bearings. Polygonal bearings, wow. Porsche uses some interesting stuff! Maybe this can help the next person that attempts to change the seal and expects these bearings to be nice and smooth.
http://www.wolfetone.com/carstuff/boxster/986%20Group%203%20Transmission-Manual.pdf