我能否先回国，再从国内入境日本。还是我只能从美国直接入境日本呢？ - 与一楼说的一样，你从哪里入境日本都没有问题，签证有效就可以了，P.S.- 在美国办理个人旅游签证绝对比在中国办理简单，我妈那存折只有一两千美元，都批了。
不过因为你是持F1的，不是绿卡，要办多样东西呢，- submit additional evidence made by an interested person (Guarantor) in Japan.
Applicants Who Need Additional Evidence
Applicants for a Temporary Visitor Visa who have a national passport of the countries listed below are required to submit additional evidence made by an interested person (Guarantor) in Japan. However, this may not apply to applicants (and their spouse and minor children) who have:
--Legal U.S. permanent residency (Green Card); or
--Legal status (U.S. visa) which allows the applicant to work in the U.S. for more than one year (excluding F and J visas) and evidence which shows the applicant has a socially and financially stable status in the U.S. (a certificate of employment, a bank statement etc.) Also, this may not apply to students or researchers of the nationality of the list A and B below, who can prove that they belong to an educational or academic institute in the U.S. and the purpose of visiting Japan is attending an academic meeting or conference.
Armenia, Azerbaijan, Belarus, Georgia, Kazakhstan, Kyrgyz, Moldova, Russia, Tajikistan, Turkmenistan, Ukraine, Uzbekistan，
People's Republic of China
http://www.ny.us.emb-japan.go.jp/en/d/03.html