What I'm trying to say is "what time is it in Japan right now?". My main problem is if I placed 今 correctly and if I should use に or は?
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に doesn't function as a locative marker (but で) because attribution is not a "static action" (which is a confusing term, I think). – user4092 Apr 3 '18 at 22:01
Most commonly and naturally, it should be:
「今日本{いまにほん}は何時{なんじ}ですか。」
You located 「今」 correctly, but used the wrong particle 「に」. A comma after the 「今」 is optional.
Also common would be:
「日本は今何時ですか。」
Finally, you can only start a sentence with 「今日本に」 when it is followed by a verb describing a stative action as in:
・「今日本にいます。」 ("I am in Japan now.")
・「今日本に住{す}んでいます」 ("I live in Japan now.")
How about 「で」, one would ask. 「で」 can be used when it is followed by an "active" (as opposed to "stative") verb. You can say:
・「今日本で大学{だいがく}に行{い}っています。」 ("I am attending college in Japan now.")
・「今日本でプログラミングの勉強{べんきょう}をしています。」 ("I am studying computer programming in Japan now.")