Not sure of the compatibility side of things and I'm not sure if a patch has ever been issued for your build to bring you up to 40040. I think Just Trains produces one based on the Auran patch. I would recommend you stick that part of the question in the S&C 2009 thread on the 2009 forum.
Certainly when downloading S&C and running build 40040, the option is given to install S&C as a stand alone or add on to TS09.
I believe that the S&C has to install into build 40040 or higher. If JustTrains haven't produced a patch yet and none of the Auran supplied ones do the job here's something you could try.
Install S&C as a standalone.
Copy the .ja files from the builtin folder in your current install into the builtin folder of the standalone S&C
Add your TS2009:WBE serial number to the standalone S&C
Do an extended database repair.