1. I will go over to Japan. [Will is stressed in this sentence.]

2. I will go over to Japan. [Will is not stressed in this sentence.]
3. I'll go over to Japan. [We can see a contracted form, "I'll" here.]
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Do we have any differences in meaning because of the state of 'will'?

I'm not sure what you're asking. If "will" is stressed, it indicates some determination, perhaps overcoming some obstacle to the trip. If it's not stressed, contracted or not, it's merely a statement of the speaker's intention to make the trip to Japan.