I've no experience with migrations beyond manually transferring the database data, but this requires correction of all view access level and usergroup usage, which can be quite a bit depending on what is installed. Directly copying database and running CB Tools will not fix this for you, you have to comb your entire site and fix it manually. This means tab access, plugin access, all access parameters (there's a lot in CBSubs, GJ, and various plugins).
I wrote a migration script for jUpgrade when it was first coming out that did this automatically, but since then I've no idea what has happened to jUpgrade to make it so unreliable.
In short it's going to take a chunk of time, but the good news is you shouldn't have to do any sort of migration again for quite some time as hopefully changes between current and future Joomla releases won't be so drastic.
Kyle (Krileon)
Community Builder Team Member
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