RoadKingKamchi: Have you noticed whether it only makes this noise after it's heated up and not when it's cold? Is it coming from the left side at the rear of the primary?
Ron

 

Hey Ron, thank you for your response. That is a great question, and I haven't noticed. By the time I get it in a place to go 55mph+ in 5th gear, she is always warm. I would say that it is definitely coming from the left side of the bike, but where exactly, I don't know, for I don't want to get too low when riding at that speed. The mechanic wasn't able to replicate the situation on a dyno, so it is only happening on the road. I can literally shift into 5th from any gear, and as long as it is in that speed range, and gas is applied at any level, it makes the noise... I am open to any thought / idea you may have...

 

Next time you are out and in fifth place a couple of fingers on the clutch lever with light pressure. If you feel the lever pulsing in and out the driveline is pulsing. It's caused from the primary trans shaft bouncing in and out and pounding on the bearing at the weak trap door of the gearbox. Conditons need to be just right for this resonance to get to that noise level, but it all starts from the longer stroked 96" engine. In order to stop it, the load needs to change, like get up to 60mph in fifth or have the cush drive ids to tame the engine pulses to a point that it won't develop even at 50 mph in fifth. The stock compensator is a major instigator at causing clatter as well, with it's wimpy spring pack feeding an impact into the trans. Even sometimes a stage 1 download will alter the engine pusles enough to eliminate it
My 07 custom was an absolute piece of crap in fifth the first year. At the time there wasn't and still is not an ids available for softails. I modified the comp spring rate and added a tmax tuner. The noise was gone for good. Recently added the SE big twin compensator and it is still silent in fifth. Not saying this is your situation, but the sound you describe sounds exactly like what I had. Dyno may not duplicate the sound as there is no wind resistance, which actually increases load on the drivetrain. Resonance requires fairly exacting parimeters.
Ron

 

What rbabos mentioned is exactly what I was trying to convey in my post above "what you are hearing may be the results of the power strokes of the 96 engine". At a certain speed in a certain gear, you can get most any bike to do pretty much like you are hearing on yours.

I doubt the dealer will find anything that will eliminate the noise in your bike. It's a weak design that is causing it in the drive train. The early 96 engines in 07 were notorious for this clatter and the IDS quieted that down.
Yours has the IDS from the factory but a good synthetic gear oil like Spectro Platinum will help the trans tremendously to run quieter and shift better. As far as the weak trap door on the 6 speeds, there's little that can be done about that aside from replacing it with a quality unit from someone like Baker trans.

 

Could it be that you may be inadvertantly operating it at too low RPM . These newer . engine and transmission combinations require a higher RPM operating range than some are used to. I would never run mine below say 2200 in any gear but first. In normal riding I seem to be in the 2200 to 3000 range up to including 5th. 6th never much below 3000. Harder without a tach, but maybe try reving it a bit more than your used to