Enjoyed reading this thread and while it went off topic at the end thought I'd add my two pence worth as there seems to be a bit of confusion.
The sticky part is that the JKA is under the WKF.
I don't think that it is accurate to say that the JKA is under to the WKF. Actually no individual associations are allowed to directly affiliate with the WKF, only national federations. (and It should be only one national federation per country)http://www.wkf.net/index.php?option=com ... &Itemid=99
The JKA is affiliated to the JKF which is the only officially recognized and sanctioned representative body for karate in Japan. The JKF is in turn affiliation to the AKF (Asian Karate Fed.) and WKF. (It is correct that the JKA played a critical role in the set up of the JKF but that is another topic.)
For info on the JKF and what it does:http://www.karatedo.co.jp/jkf/jkf-eng/e_index.htm
and here for the structure of affiliated organizations:http://www.karatedo.co.jp/index3.htm
(there used to be a better link but it doesn't work)
JKA members can compete at WKF tournaments only IF they are chosen as a member of the national team by the JKF, because of their JKF affiliation not JKA affiliation (same applies for members of the SKIF, JKS, or other shotokan organization). Pretty much every competing trad. karate athlete in Japan has to register with the JKF or they can't compete (includes all elementary school, Junior high school, Senior high school and university students, the bulk of competitors).
JKF affiliates' tournaments (including those of the JKA) have to be approved by the JKF, before they can be carried out though the competitors for association tournaments do not necessarily need JKF affiliation though many do have it if they compete in other tournaments. It also makes insurance a hell of a lot easier.
Basically, if a tradition karate club or association (meaning the big four styles) is not affiliated with the JKF then it is not officially recognized, nor are any grades outside of the JKF (JKA members are lucky in that their JKA rank up to third dan can be directly converted to a JKF rank without re-examination but that does not apply to a WKF rank).
Though I went a bit off topic as well, I hope this clarifies the situation that the JKA is not under the WKF, at least not directly and only by proxy.
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