Hi @flinstoning
I'm sorry to hear about your situation.
I would like to inform you that once you merged your account, you selected the wrong server where you had no progress. That have lead you to restart your story and, as the merge automatically reordered your Pokémon in a random way, you finished to play the Kanto's story with a Johto's Pokémon in your team.
As you know, you cannot use the Pokémon native other regions while you are playing a specific region, and therefore they should be locked in you rPC until you would have obtained the 8th badge of the current region you are playing. Therefore, all the Pokémon you may have in your party that are not native of Kanto, in this case alakazam, are currently stuck in your team.
Before proceeding in moving in your PC your stuck Pokèmon i would like to ask you if you would like to unmerge your account in order to get back all your story-progress or if you would like instead to continue with your current progress and re-do the story.
Please, in case you should decide to unmerge, refrain from doing any trade on the silver server, as that would made you not anymore eligible for the unmerge.
Looking forward to your reply, have a wonderful day !