Don't worry, be happy

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I don't think you have to worry about it fitting in a container. Mine came over from Japan in a container with 33's and a roof rack on. The container will either be 8' or 10' tall. Likely 10'. If you ship by container, you also don't need to be worried about anything going missing from your truck. It's much more secure than shipping RoRo. RoRo lots of people have access to your vehicle while it's waiting in Japan to be shipped out, while it's on the voyage over and when it's waiting to get picked up on this side.
As others have said, you also don't have to worry about getting it on the road here. If your Shaken is up to date, you'll probably only have to get E code or DOT marked headlights to get it to pass inspection over here.
I'd bet for the most part you could get parts for the Jimny here. Maybe not body panels, but you could likely track down other general maintenance stuff.