There was a good discussion of this migration topic back when the previous version of the Sony software came out, see:
https://www.mobileread.com/forums/showthread.php?t=34764
To recap the reader file hiding places (All these references presume you have WinXP and have used the Tools tab > Folder Options > View tab to turn on "Show hidden files and folders"):
The default place for books (I think it's the default):
C:\Documents and Settings\{username}\My Documents\My Books\eBooks
There is the program itself, with all it's unique identifier certificates, in:
C:\Program Files\Sony\Reader
Then there is the database in:
C:\Documents and Settings\{username}\Local Settings\Application Data\Sony Corporation\eBook Library\Database
Some LRFs live in this directory as well.
Then there is the registration/setup stuff in:
C:\Documents and Settings\All Users\Application Data\Marlin and
C:\Documents and Settings\All Users\Application Data\kinoma