Scince most of you sound like you know your chit, I need your opinion. I want to have a 6 speed tranny installed in my 03 SERK. What tranny, if you were to do this yourself ? Baker...........H.D. 
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Why do you want to change your trans? Do you have to because of problems with your stock trans?
I have both a Screamin Eagle 6-speed and the DD-6.
IMHO it is not worth the money in changing to a 6-speed....If you want to save money on fuel...lit will take over 100,000 miles to recoup the investment........If you think that lowering the rpm's will help save our engine.....the worst thing you can do to a twin cam is to run it at too low an rpm. You lug the motor, doing undo stress on the internal parts.
The DD-6 uses a 28 tooth comp sprocket. This helps in creating a direct drive for 6th gear. Making it actually more efficient. This is the better of the two for touring. IMO
The SE 6 speed....once you change to this you can't go back. Grinding of the case is in order....Alot of people change out their primary gearing to a 24-37 set up. This is the better of the two for a bar hopper. IMO
Good luck, but if it were me....wouldn't waste the money