Our son was supposed to get braces later this month.  They have been waiting for two teeth to come in, and they finally are.  Looking at the dental info at Yoko hospital as well as  the overseas screening  forms they says if braces are put on after the date on the orders they will not provide care. 

Will they put on braces in Yokosuka if we wait until after we arrive?  If not, has anyone used a Japanese orthodontist, and have any idea of the cost?  

There is an orthodontic clinic, but I think you have to be referred by the general dentists. That is how we got in. I think active duty has easier access. I know that some civilian families do use Japanese orthodontists as well.

The dental clinic will provide you a list of English speaking dental locations.

I recently visited one:
http://www2.gol.com/users/tward/map.htm

The fees are about double, crowns=2,000, root canal=2,000 I don't know of any coverage that pays 100% for the more difficult procedures, I researched them all.

I am in the process of getting my son's mouth fixed...He doesn't have the space for teeth to come in and will have to get some pulled before it's all said and done...I have been asking for 1 1/2 yrs for him to get a referral to ortho and have been blown off...Finally, this past Jan...Dr. stein peaked in on him during his routine exam...He agrees he needs help...Come back in 6 months as your son has more baby teeth that need to come out...We go back in June...was told come back in Jan 2012....they called us to come in August to get pictures and more xrays...He is now on a waiting list for care...4 to 6 months or longer depending on the needs of the clinic and I guess how severe others are...My son was graded as an 8 to 10 for his problems...He needs help in the worse way...now we wait...Good luck in getting care...My friend brought her daughter over with braces and she was given care but got a good chewing saying she was trying to get free care...that was not the case as the paid over 5 grand to get those braces on and that is after tricare paid their portion.
You can go off base and tricare will pay you back and that takes about 2 months to get a payment and you will need a local bank(ie. NFCU or community bank) to deposit the check.