Migrating from one structure/site to another can be a complex process. I have certainly found within my new role, where I have been migrating 30+ sites to one drupal multisite installation that the process of moving sites is a convuluted one. Not only can it require the migration of databases, but also the procesig of strings to sanitise them ready for implmentation into a new database system and structure, especially when having to split strings.
Therefore I intend to be investigating far more into how to smooth the process of database migration, especially into Drupal (my current fave CMS). I have been hacking away at a few scripts, especially for changing links and date/time strings into drupalised strings with differing sucesses. I presume only time will tell. Possibly I could suggest new alterations to drupal migration scripts, to allow far more configurability of your data. Check it out soon.