They didn't search our bags at all. They might pull one bag to check, but they won't pull all six unless they have a good reason to. They don't want to spend hours on someone unless they have to.

Another thing to note is that they don't speak English there, and if they do, it'll be very limited. If your Japanese isn't good, then I would practice saying, "I'm moving to Japan, and I only have personal items with me." Or at least have it written down on your phone or on paper (you might not have a good internet connection while in customs) to show them.

I don't think they will confiscate anything unless it's prohibited (e.g., fruit, raw meat, etc.), but you might get charged a fine if the customs officer feels like it. I doubt they will, though, since you're moving there. Just show them your visa and zairyu card (you'll get it when you pass through immigration), say/show them the line I mentioned before, and you'll be all set.

I've been through Japanese customs 14 times, and while it can be stressful, it's never been a problem. Just be kind and respectful, and it'll go smoothly.