After looking for an analysis on Jazz Improvisation I finally found one that looks promising. I will update this entry when I worked through it for now the link to the pdf:
http://web.njit.edu/~mendonca/papers/jazzimp.pdf
Update1: While great in the introduction this paper is a little too specific on the research and a little short on the subject of inmprovision itself. Yet still an enlightning fast read.
I am still very open for any tips on good articles about fundamental theory of improvisation in general if you have one, please post it in the comments.
Update2: There is a blog that talk about improvisions - in all aspekts http://www.appliedimprov.net/