The patient will be given 6 doses of chemotherapy with a drug called Ara C in high doses (every 12 hours) which will begin 8 days before their stem cell transplant. Then, another chemotherapy drug called cyclophosphamide will be given in high doses by vein for two days on the 7th and 6th days before their transplant. A drug called MESNA will be given with cyclophosphamide. MESNA is used to decrease the side effects caused by cyclophosphamide. Radiation treatment will be given to the entire body on each day for 4 days before the transplant. This will be done 2 times a day for 4 days. The chemotherapy and radiation treatment will last 8 days. The patient will receive extra radiation treatment if they have certain diseases (central nervous system (CNS) disease, testicular disease or other focal (localized) disease).