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If the problem is still relevant for you I can recommend cart2cart as an option.
I have recently done the migration to multi store. Here is the detailed instruction on how it actually works with magento: http://www.shopping-cart-migration.com/magento-multi-store-migration
I know that you need an update however you can simply perform it with migration on new updated installation and avoid much issues. multi store is not the easiest feature to manage so if I were you I wouldn’t risk to do it on your own.