Thanks for the kind words everyone.
It has been a particularly sad time for my wife. She loved her father very much, and will miss him. She has often spoken fondly of him throughout our 19 year marriage. He was a very kind and gentle father, rarely raising his voice at her. He has been generous to the both of us, providing help when we needed it during our move to Japan and then five years later when we relocated back to the U.S.
Regarding the waiting time for the ashes, it is actually a 49 day wait (called shi juu nichi) until her family receives his ashes - not 90 days. I couldn't find a resource in the internet (especially Wikipedia) that gives a great explaination for the 49 day wait, but my wife tells me that in the traditional form of Zen Buddhism that Japan follows, the soul takes 49 days for Joubutsu to occur. Joubutsu means enter Nirvana, become a Buddha, go to heaven.
While nearly all Japanese practice a form of Zen Buddhism, there are many sects, and I gather each has a slightly different ceremony, particularly in the chants the Budhhist priests chant.
My wife's father's family have all practiced the Shingon sect, and that is the ceremony that was performed.
Here is a Wikipedia link to Shingon Buddhism:
http://en.wikipedia.org/wiki/Shingon
Here is a Wikipedia link on Japanese Funerals:
http://en.wikipedia.org/wiki/Japanese_funeral
It pretty closely describes how the funeral was carried out.
Well.......the week has gone by in a flash. Right now it's just after 10:00 p.m. Monday night in Japan, and we are heading back to California tomorrow afternoon.
I have to reiterate how deeply touching the whole ceremony was. Having studied Buddhism when I was a Religious Studies major at university, I came to feel a closeness and respect for Buddhist and related Eastern thought. Some of its insights (such as having few or no expectations) have benefited me greatly in life. Of the greatest importance, is that it also lead me to Japan, where I found and married my wife.
As crazy as it sounds, I still relate to the whole Richard Chamberlain character "Anjin san" in the Shogun book and movie by James Clavell. The book Shogun is loosely based on the true story of the first Westerners to land on the Japanese soil in about the year 1600 to do missionary work as well as bring back its riches to Europe.
As the only Westerner everywhere I went, you stand out like a Martian. And being a fluent Japanese speaker, people just about jump out of their chairs and can't stop staring at me. As the funeral proceeded, I was expected to go up and perform whatever ritual was expected, which I had no preparation for. Luckily, I was in the first row, and could quickly watch the moves and the words that were said, and then I would repeat them. The other guest at the funeral thought these were things I already knew, yet I was just parrotting them as the funeral developed.
All in all, I really believe I've had a singularly intersting life experiences so far, far exceeding my age of 40 years.
I'm sure I'll continue to "marinade" in the events of this experience for a while until I can really get my arms around it.