I would add my voice to the ones supporting you on expressing yourself and being open to finding your way, but I thought instead I'd raise some issues that hit me while reading your questions.
The first thing that struck me was that while you were once sure of your Way as an Atheist your are now becoming sure of your Way in AiKi. I wonder whether it would not be wise to see how temporal our beliefs are, and to remain open to the possibility that this, too, is a phase you will pass through. Just as the letting go of your Atheist past is made harder because of the way you clung to it and allowed it to mix up with your sense of self, so here, also, you are in danger (perhaps) of losing your Self in your Beliefs.
I guess that, for myself, I hope that AiKiDo will not be my final opportunity to discover that reality is much larger and more intersting than I had previously thought.
A second issue that came to mind reading your post is that while there is much to admire about Japanese culture, there is also much to abhor. While there have been long arguments back and forth about whether the Germans were 'culturally' suited for fascism or whether it happened there accidentally, fewer such arguments arise regarding Japan. The willingness to revere and to make our own selves small in the faith of Traditions, Customs, and even Objects can have many uncomfortable and even fundamentally evil consequences. I also have a deep respect for the Japanese sensibilities and aesthetics (such as I've experienced them), but I think it is important not to forget the other side.
Anyway, that's enough for now. Good luck on your way.