The main purposes of this study are to test the safety, clinical benefit, and bioactivity of vaccine therapy in combination with Cyclophosphamide and Trastuzumab in patients with HER-2/neu-overexpressing Stage IV breast cancer. This study will also to test whether the Cyclophosphamide can eliminate the suppressive influence of regulatory T cells, and whether Trastuzumab can increase antigen processing and presentation. These drug activities may make the immune system react better and enhance the effects of the vaccine in treating breast cancer.