The stainless body is the same. Propulsion, braking, doors, interiors and other componets were new or rebuilt to new condition. Think of it as a R62/R68 (1980s technology) in a 1964 body.
11-car operation began on the Flushing Line just prior to the 1964 World's Fair, as the new R33/R36 cars were being phased in.
See this NY Times article from 1963.