While the import toolkit is fantastic to move data between systems, for custom tweaking, you may want to create your own application to clean and manipulate the data in Kentico.
For what it's worth, I too looked at doing SQL tweaks to create/delete/update things, but I was worried I'd hose the database... but I tried anyway and ended up loosing an hour of work when I realized that my development db didn't work anymore - I was importing documents and had broken the tree... luckily I'd backed up the db just prior to doing my foolishness!
So I swiftly moved over to using the API. FYI - The Kentico API allows you to do pretty much anything you can think of to the Kentico objects. So I created a little console project to read the source db and the destination kentico db and manipulate and tweak the objects as I needed them. I have about 6000 documents to play with, so doing anything by hand (using the backoffice) was out of the question.
See
how to use the API here.See
using Kentico API outside of the Kentico application.Good Luck,
Lance
PS - it helps if you have access to the Kentico 'source' so you can look up how to do certain things the way the Kentico guru's do it.