While account-wide pets and mounts will be going live with patch 5.0.4, the exact process involved has still been somewhat muddled. Game Designer Cory "Mumper" Stockton clarified the process somewhat in a post about battle pets yesterday. While pets that are unique, such as achievement, pet store, promotional and guild pets, will be combined into one pet in your UI, others will have duplicates available.
Because of the nature of the merge, these duplicates will bypass the rule that only three pets of one type can be had with the new pet system. Any duplicates you have that can be caged will be tradeable, or you can simply release anything you don't wish to keep. This news should be a welcome relief to pet collectors who have multiples of the same pet on many different characters.
Pets will still be merged on MoP launch, but instead of placing them in your bags or mail they will be placed directly in your pet journal. You will be allowed to have more than 500 and 3x per pet during this process. Any pets that are flagged as unique will be merged into one and also placed in your journal. (Unique pets are from Achievements, Pet Store, Promotions and Guild) You will be able to cage any pets that are tradeable and you can release anything that you have more than one of.
A few examples:
A B.net account has a total of 6 Wolvar Pups across all of it's characters. On merge the B.net account would have 6 Wolvar Pups. This would be the only time an account is allowed to have more than 3x of a single pet.
A B.net account has a total of 3 Murky's from BlizzCon 2005 and 4 Nuts from the pet collection achievements across all of it's characters. (both unique pets) On merge the B.net account will have 1 Murky and 1 Nuts.
Hope that helps clear things up.
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