"We are building towards the World Cup at home and the first step is to be among the top 10 nations by 2015," affirms JRFU chairman Tatsuzo Yabe. "Then we want to be in the final eight teams when the tournament comes to Japan."
As well as the weight of an inglorious history, Japan also have to contend with a fragmented domestic structure, an indifferent public and obvious physical challenges.
"Argentina took 12 years (to move into the top 10)," says Jones, "and we are trying to do it in three. It's tough but we have some advantages compared to other tier two nations. Over 500 universities play rugby here and we have a club competition (Top League), with some of the biggest companies in the world putting teams on the field. I don't think the international performances reflect the infrastructure in the country."
Jones, whose mother is Japanese, first worked in Japan in 1997 as coach of a university team and the following year was appointed forwards coach of the national side. He has since had two spells at top Tokyo club Suntory before his appointment to the top national job. He says an absolute imperative is the formation of a uniquely Japanese style, which relies on a quick-passing, high-tempo game that he compares to the Spanish football team.
"We have got to be like Spain in football," says Jones. "In a typical match they pass the ball six times more than the opposition. Their midfield are all small but it doesn't matter; sure, football is a different game but we need to think exactly the same. We will never be the biggest side in the world so we need to move the ball quickly - in contact, out of contact and before contact."
Jones acknowledges the profound Kiwi influence on the sport here but says there are problems trying to ape the winningest nation in world rugby.
"The New Zealanders have had a great influence and have brought a lot of good things here," says Jones, "But one of the bad things is that the Japanese have tried to copy the New Zealanders - and you can't. The only team that can play a New Zealand style is New Zealand.
"We have to find our own way. As an example, in terms of scrummaging, we should look at France because they also have smaller props like us.
"They get low, race into it and are really aggressive. That is how we should be scrummaging, not like a New Zealand side that relies on bigger props."
Jones claims that before rugby turned professional, Japan was one of the world's most inventive teams: "I played against Japan schoolboys in 1978 and they were using two-man lineouts and quick channels into the scrum - no one else did that. Since then, rugby here has become so orthodox."
After the under-20 side lost 120-0 to Wales this year, Jones assembled some of the leading coaches and high performance people in the country to seek explanations. One of the more unusual offered was that Japan rugby retains a 'rice farmers' mentality.
"Fifty years ago, half the nation were rice farmers," explains Jones. "There was one guy in charge of a village and everyone had to do what he said and follow orders. If you didn't, you were kicked out. But I don't buy that now and our players can definitely think for themselves."
The elephant in the room remains the lack of, uh, elephants in Japanese rugby. Japan remains one of the smaller teams in world rugby.
Jones has employed an ex-UFC fighter to teach them about being quicker in contact, which he says gives someone a good chance despite being 10kg lighter.
With former Brumbies and Wallabies trainer John Pryor on board, he also hopes to make his team the fittest in the game.
"Against Georgia recently, we gave them 80-90kg in the forwards," says Jones. "The first 30 minutes, we got physically hammered but we came back from that and won the game in the last minute."
Jones regularly pays tribute to the work of Kirwan, who he says raised Japan to a new level. But his approach to foreign players is markedly different.
"I've cut out half the foreigners," says Jones. "We'll have two or three on the field and within the 30 have five or six - but they need to be part of the cohesive team. I think there were probably too many foreigners in the past and it really affected the way that they played. They played very traditionally, in an orthodox sense, and we can't win like that."
It is a brave stance by Jones. Football minnows Qatar, who are hosting the Fifa World Cup in 2022, long ago recognised their shortcomings on the field and are naturalising as many Brazilians and Africans as they can now, so that in a decade at home they will be competitive.
For now, after a difficult start (Japan lost all three matches at the 2012 Pacific Nations Cup and both home matches against the French Barbarians), Jones was basking in the afterglow of Japan's successes on the recent European tour, where they toppled Georgia (18th) and Romania (15th) for their first wins in Europe after 26 consecutive losses.
Their last tour there - in 2004 - was a dismal failure, with a 100-8 loss to Wales and a 98-0 thrashing by Scotland. Jones wants to visit more often, as part of a deliberate strategy to get used to playing in Europe ahead of 2015.
They also hope to engage more quality opposition on a regular basis; giant banners already hang outside the national stadium promoting next June's visit by Wales.
"I'm trying to 'Japanese' Japanese rugby but do it through world class principles," says Jones. "Results will be up and down but by 2015, we will have a good team. I'll finish in 2015 and want to leave a team that is respected around the world for the way we play."Michael Burgess travelled to Japan with the assistance of the Asia New Zealand Foundation.