The designated recipient for purposes of Chapter 53 (commencing with Section 5301) of Subtitle III of Title 49 of the United States Code shall be the San Diego Association of Governments, and it shall be responsible for allocating federal transit funds to eligible recipients. The board shall prepare the program of projects for transit capital and operating assistance projects in its area of jurisdiction for receipt of federal funds. The San Diego Association of Governments shall allocate the funds to the board to fund its projects. If a dispute regarding the allocation of funds arises between the board and the North San Diego County Transit Development Board, the two boards shall negotiate in good faith to resolve the dispute. If the negotiation does not result in resolving the dispute prior to adoption of the annual regional transportation improvement program, the San Diego Association of Governments shall resolve the dispute and allocate the funds accordingly.