Not sure if this really helps but did you check condition of the linkage? If I recall the linkage and then metronics seal (big round plug going into the trans) are right near each other. If you had lots a lot of fluid from the seal (it's a common slow leaker) then maybe somehow it gummed up the linkage ?
Did you drop the valve body when you cleaned your fluid? If so then there maybe other possibilities of the shift linkage pin alignment (see step 8 in the pdf).
Again, both of these are pure guesses, perhaps someone who has experienced or more knowledgable will chime in.
http://www.xoutpost.com/attachments/...eplacement.pdf