Difficulty of communication with people varies greatly depending on who you talk to and both how strong your Japanese is and their English is. That and whether or not they speak in heavy dialect (which is kind of common in the area in Kansai where I am unfortunately).
In and around campus/the dorms no, I really don't have any trouble communicating with people. Most of the Japanese students are really into meeting and hanging out with exchange students and really enjoy practicing their English with foreign students as well as helping foreigners practice their Japanese. I can't really speak for other programs but I'm sure most of them are this way. Outside of campus though, when we're out adventuring and doing whatever, communication can get tougher since people you talk to very rarely have any English to use as a safety net if there's a language stop gap. Usually isn't a problem though because there are people that I hang out with of all different levels of Japanese mastery so there's usually someone there who is either good enough at speaking Japanese (or most of the time just a Japanese friend) who can bridge communication gaps.
Communication is definitely the biggest challenge out here but it isn't like devastating hard or frustrating. It's just a challenge.
As for food, yeah you'd be surprised. There is plenty of non-seafood food here, but I'd be lying to you if I said seafood wasn't the predominant cuisine. That majority of restaurants you'll likely encounter specialize in fish dishes and what have you, and sushi is practically ubiquitous so not being open to any seafood will certainly severely limit your options, but it is definitely possible and within reason to spend extended time in Japan and not eat seafood. Sushi might not be nearly as popular in America, but that doesn't mean you can't get it. Same way with most red meats and such in Japan. You can find 'em, but they just aren't as popular as in the states so you will see them less and typically need to pay more to get 'em.
You'd probably only have cuisine issues in Japan if you couldn't handle rice, udon noodles, or ramen noodles. If that was the case you'd be pretty much ****ed lol.
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