Make sure you have a backup before the migration. Then make a backup of the backup.
Use your VAR to handle the database migration which will include the custom CC stuff.
Use task Scheduler to migrate your files. We only batch process Library files and handle Project files as we open them, mainly because they are historic and not used every day like Library files (we have 2 project files, Library and Projects). Task Scheduler can be a bit of a pain so only migrate about 500 files at a time. It can be run on several machines concurrently though to help speed things up. Best to do overnight when no other user is accessing the database.
We have done this 4 times now with minimal troubles. 1 key note is when using Task Scheduler and migrating IDW files to look at the options and consider the SET DEFER UPDATE setting (I think I have it named wrong but you will find it). In some versions it is on by default so after the migration each time an IDW is opened it gives a warning message and you have to manually turn the DEFER UPDATES off. A pain for the unknowing.
Best of luck. I will be going through this again next Feb for 2012 to 2013 upgrade.