The 4-1 header is designed to give you power in the very high rpm range. The 4-2-1 header is designed to give you power in the low-medium rpm range, which is much more usefull on the street. If you bought a 4-1 header, your stock motor in your application would be nearly redlined before you noticed some or any of the benefits. Go with the 4-2-1.
As far as improving the performance of a car with an auto-tranny, look into buying a level 10 torque converter. I'm not sure if they make one for your car, but if they do it would be a big improvement. I'm not sure where to purchase one, but I'm sure someone will reply to this post with a link.