I'd just recommend using a male, guy, boyfriend etc. with no special meaning of him actually not being physically fully a guy. As he feels that he is a guy, so associating him with male words would be the way to go.
Though, the best might be to ask him what he wants to be called, but I'm rather sure the answer would be the male pronouns.
Knowing that there is a language barrier, I don't think he will mind you not using Japanese for everything. it is understand considering you two are from two different cultures and from my own experience Japanese are rather understanding with foreigners, if they can't get everything right the first time. So just take it calmly and try not to think about this matter so much. In the end, his only a guy in a body a wrong body, so besides under rare circumstances I don't think he'd want to be mentioned anything about her female body.
Just remember, one can't learn a language over night, so ask him I'm sure he will be glad to help you out with your Japanese skills. I never had any issues with Japanese not being helpful if I had some questions about Japanese when I lived there.