There is not much difference between the 2 flex pipes, only about 1/2 inch in length. But I would be more worried about the transmission slipping in 3rd gear.
What did you spray on the head bolts?Yes the OBX is available for your 06 automatic, it has a slightly different flexpipe then the manual transmission. I know because I have both flexs that come with it and have the OBX header installed in the car. I have the automatic flex pipe sitting around here somewhere brand new if you need one.