There are two ways you could do this.
1)
For the email reason and some other differences between 5.5 and 5.6, you should upgrade first to 5.6, then to 6.0.
Then temporarily move your ibays folder to /tmp, then do a "backup to desktop" (not backup2ws), which will include all your user and home folders and email (now correctly migrated) as well as config data (resultant backup file needs to be less than 2Gb). Then use this file to restore to your new 6.0 box. The config that you don't want can simply be deleted or amended using the Configuration screen and server manager.
2)
Use the Lazy Admin Tools, available in the ocntribs section to transfer your users etc. You will probably need to play around with user mail folders though. You will also need to copy and restore the user email data, probably gets a bit messy, that's why option 1) seems easier to me.