My understanding is MSCRM_CONFIG holds server-related settings e.g. where is SQL Server?, not customisations. What was the old metabase is now held in the main database. Therefore, the changes you made should have come across in the original restoration. If they didn't the only thing I can think of is they weren't published and somehow got dropped.
The upshot is you shouldn't migrate the CONFIG DB.
Leon Tribe
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Want to hear me talk about all things CRM? Check out my blog
http://leontribe.blogspot.com/ or hear me tweet @leontribe