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I have an auto too and was told that you need to modify ( grind ) the long tubes somewhere to me'em fit properly, i think it was the passanger side. If you get em let me know how it goes as this is on my list to do
Depending on what brand of longtubes their is no fitment issue with auto tranny. I know mac fits it.
You can not reuse the hpipe on longtubes and shorties arnt worth the money they cost.