I am in this situation myself right now and have just completed rerouting with US.
I am in New Zealand now, flying home to the US on Sunday 3/20 on a biz class award ticket. Yes travel has commenced and I am halfway through the ticket.
US has issued a travel waiver for codeshare / partner flights going through Japan through March 31, making possible even changes to award travel already in progress. (You will sometimes find an agent who does not believe this, so either call back or ask them to ask the supervisor.)
I found reroutings through Sydney, Bangkok, and Tokyo-NRT back to the United States, using the ANA tool, expertflyer, and UA's website.
When I called, I found that the requirement was to have "saver" award tickets available in the same class of service (business in my case).
To make a long story short, I was able to cancel one of my flights on ANA and rebook it on a UA flight without any penalties. I also changed the leg following that (originally was LAX-PHX, now is SEA-PHX).
Because the award ticket was issued by US, they are the ones responsible for reticketing it. It is luck of the draw as to which agent you get, but if you specifically TELL them that US has also issued a travel waiver for Japan (even though they don't fly there directly), you should be able to have the tickets changed, or at least eliminate the two day stopover and just make a short layover or change of planes in NRT.
GOOD LUCK and let us know what happens!
Jason