Cirrus,
Your somewhat bad luck with the whole thing might turn me off of doing my swap... Not that I already have all the stuff to do it, but I am seriously thinking about it... I have this nagging voice in my head telling me to get rid of the Auto tranny!....
Some how I though it would be much easier than what you have described in the process though... and your current issues with the clutch and whatnot...
Man I seriously hope you get it figured out and that it turns out it was something not related to installation or swap, but a faulty part!...