"Whenever I accelerate there is a horrible whining noise. It is there at idle too..I just gets higher pitched with acceleration."

MAke sure the ground to the amp is less than 15" and is grounded good. Turn the gais on the amp down a bit, and if that doesnt work get a better amp or put an inline noise filter in with the power. Also make sure the shop ran the power and rca cable opposite of each other.