The reason free trade doesn't exist is because of tariffs and other barriers. Erecting more barriers doesn't make trade more free. It does exactly the opposite.
The stupid thing about trade barriers is that they hurt both sides. When Japan restricts trade, it hurts us and them. When we restrict trade in return, it hurts us and them again. We can't do a whole lot about the first part, but we can and should avoid the second part. Trump says that trade wars are easy to win. In fact, they are impossible to win because there are no winners, only losers. The only way to win is not to play. Just because Japan is stupid, that doesn't mean that we should also be stupid.
We run huge trade deficits with other countries (including China) because of an accounting artifact that counts money flowing back and forth for the purchase of goods, but not money flowing back and forth for investments. The Chinese buy more American bonds (and stocks and real estate, etc.) than the other way around, so we have a trade deficit. It's a completely separate issue from free trade.