Hello mattjapanquestio:

The answer to your question is yes.  The stipend you received for graduate studies (or research) conducted in Japan is taxable income . . . to the extent that the money received was not used directly to pay for university courses or fees (at Texas A&M or a cooperating school in Japan, granting transferable credit toward your degree program).  It does not matter that you received this income from a Japanese institution, or from a United States source.  For US income tax purposes, it is still taxable in the same way.

Thus, to do so, please follow the general instructions and example provided at this AnswerXchange post, for entering taxable graduate stipends, fellowships, and grants:

https://ttlc.intuit.com/questions/3802027

It does not matter here if you received a Form 1099-MISC, or not.  You may have a letter, statement, or some other documentation that your Japanese benefactor sent you; or perhaps you don't.  The answer to that point is really not important, as this income is still taxable in the very same way, notwithstanding how it may have been reported to you.

Thank you for asking about this important matter; and good luck with your academic activities.