Runner, I've been to Japan and loved it. In fact, we're planning on taking the boys to Disneyland there next year, even though the LA one would be cheaper. Love the people, it's easy to get around and just an interesting place to visit. If we go next year though, we'll only be going to Disneyland and maybe a few other Tokyo places like the Ueno Zoo. Ben will only be three and I think it would be a bit much to travel around with two babies. Might be a bit easier for you with Logan being a bit older though.
If you have any specific questions, feel free to PM me and I'll see if I can help