Just out of curiosity. If I had booked my ticket through JL from new york through to chitose as one itinerary, would the domestic portion limit be the same as international business class?

I wouldn't have done this anyway, because the ticket price would have been like $1000 more. By booking my international ticket separately, I was then able to buy one of the special visit japan fares for $200 round trip. I'm pretty sure I won't be paying $1000 in excess baggage fees :-)