Is it possible for dan ranks awarded independently of aikikai, to be registered with the aikikai? If so, would I have to leave my current sensei in order to do that?
I see two possibilities:
You can become member of a aikikai affiliated organisation which doesn't only accept dojo or school as whole as members but also accepts individuals. So it doesn't require your teacher to be also a member of it.
This is the case in the aikido federation which I am a member of.
Second possibility is to ask a shihan - maybe shihan A or B would do so? - to directly submit your application form.
This I have witnessed this also.
I heard of scenario with a gentleman who was a yoshinkai shodan, he then tested for nidan with an aikikai affiliated group, paid the shodan and nidan test fees, but aikikai only sent him a shodan certificate and said that he has to wait the minimum required time before they will mail out his nidan certificate.
This is the way when you get tested with the "next" grade in an aikikai organisation:
You have to register your shodan first an you will receive your nidan ceritificate two years after shodan registration.
Might I have to go through the same thing?
I am not sure: But I think like philipsmith already said that you have to register shodan and wait and so on.
As far as I know only yudansha who did their gradings in an aikikai affiliated federation but didn't register it in Tokyo can register all their graduations in one step.