 Under the amnesty program, 3.1 million illegal aliens applied for legal status, which was 2.6 million more than federal officials expected would apply, Austin said. Agricultural workers had to apply for amnesty by Nov.  30, 1988, and other illegal aliens had to apply by May 4, 1988.  Austin said, ''We legalized more people in that program than in all other amnesty programs in all other nations combined. It was certainly numerically a success.'