im extending my mud only samuri frame this year and really dont wanna run a longer exsaust.  I was wanting to know if a doug thorley header flange will line up if flipped upside down and just run some pipe out the hood. Thanks didnt know if anyone has done this before or not.

Nope the flange can not be flipped. You will need to cut the primary tubes close to the flange, flip the pipes 180 degrees and reweld the pipes.