Hey all thanks for the helpful advice so far! I told her to adjust her plans so that while her first trip may be 60 days, her subsequent trips should be a month or less at a time, and she was OK with that.
We do have an accountant and an immigration lawyer who assisted my wife on her options to go visit the kids etc., which is how we ended up at filing the I-130. Since I also make a decent chunk from a passive business in the US, I have been simultaneously paying both federal and state taxes, as well as Japanese taxes here, for over the past decade. I have had to deal with foreign earned income/tax credits, so that's definitely on my radar.
Re my wife's ties to Japan, well she's got several million (in US value) in her name here, including the house we currently live in and a separate "vacation home" that we go to for fishing. It also has a farm attached to it that sells produce and cute little bonsai trees. Literally all of her family is here as well, as well as her dogs. She, as the eldest child, also stands to inherit a lot from her parents. No job though, since she's retired and doesn't need the money. I told her to take documentation and photos with her just in case they ask.
Just to rant a bit, my wife actually gives me a lot of ####### for being a US citizen lol. She says we wouldn't have "lost our kids" to America if I wasn't a citizen, and blames me for putting her in this position. Believe it or not, a lot of Japanese believe Japan is the greatest county in the world, absolutely refuse to learn any English, and so few consider emigrating to the US to be a good option, which is probably why so few Japanese end up in America. So while I do get the skepticsm here that we may be trying to skirt some rules, trust me, my wife really doesn't want to go to America or become a US citizen lol. But as I said, we're doing this to be closer to the kids and not end up as empty nesters. And I don't want my wife to blame me even more if she ends up being mistreated in secondary or denied entry, which is why I'm here trying to come up with a script for her to memorize and practice before she goes!