It sounds like things are continuing apace for moving to prodops and thence to Japan. Talked to potential-boss's boss yesterday; I think I ameliorated his concerns. The Japanese Embassy in Tokyo says this about visas:
What you have to do is to contact the Ministry of Justice through a contact person at Yahoo!'s Japan office and to ask them for requirements for a Certificate of Eligibility. It usually takes one to three months to get approved after you submitted necessary documents.Note that this will involve shuffling paper back and forth between here and there. Good thing that I didn't want to get there before June at the earliest.
Then, you have to bring a Certificate of Eligibility with other documents to our office and apply for a working visa after you received it from Japan. The visa will be issued within three business days if everything is in order.