Another promotion in 2003 led to him becoming engineering director for Honda Racing Developments Ltd., and he stayed in this role until 2006.

During 2006, Nakamoto got his big break being appointed the Senior Technical Director for the Honda F1 team, taking over from Geoff Willis, an aerodynamics specialist.

The RA107 was even inferior to the Super Aguri SA07, a re-worked model of Willis' Honda RA106 from the previous season.

One was that the wind tunnel which was set up in July, 2006[1] broke at almost the same time that Geoff Willis was replaced by Nakamoto.

To try to fix the aerodynamics problems Honda employed a number of new aerodynamicists including Loïc Bigois,[3] John Owen (ex-BMW Sauber),[3] Ben Agathangelou (ex-Red Bull), Peter Coysh (ex-McLaren) and Francois Martinet (ex-Williams)[3] in July 2007.