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From 2004 to 2007, our university ran a three-year project called 'GP Project' as part of a national project named "Selected Efforts of the Distinctive University Education Support Program (Good Practice Project)", with the support of the Japanese Ministry of Education, Culture, Sports, Science and Technology. In this project, we are replacing more than 30 existing courses with e-Learning. The courses must be integrated seamlessly into the course grade information system currently in use in the educational affairs section. For this integration, we introduced a new Learning Management System, which is easy to customise. We developed a Learning Management System (LMS) by modifying a commercial LMS, WebClass, to which it is easy to add new functions. The first-phase system has been implemented and we are now preparing to integrate the course grade information into the LMS. This paper describes our current three-year university-wide project and then explains the functions of the newly developed LMS. This system supports registration, authoring and importing information from different sections of educational affairs. This allows effective pedagogical activities, including mentoring/coaching through utilising Digital Portfolio (e-Karte). This three-year project with the LMS has facilitated development of a method of organisational knowledge management and e-Pedagogy.