I've got a 2006 Low Rider. 29,200 miles in exactly 3 years. Right now my bike is in pieces all over the house. I'm waiting on a new shifter drum to be delivered.
It all started 08/31 when I downshifted and the shifter was ineffective in trying to go one more gear down. It just bounced up and down. I let out the clutch and rolled it a little farther and it finally downshifted all the way down.
The next day starting out for work I hit the highway in front of the house and when I tried to shift to 2nd, it went to neutral. 1st, neutral, that was it. I made the block and parked it.
Being out of town from the 2nd to the 5th, I couldn't get back to it until later. When I did inspect it, I checked the shifter assembly to make sure nothing was preventing a full range of motion. It checked out. I pulled the transmission top inspection plate and found that when shifting from neutral to first, the shifter ratchet worked normally on the shifter drum. When going from 1st to neutral, the shifter ratchet worked normally as did the shifter drum. When trying to go from 1st to 2nd, the ratchet would work the drum to neutral and then it was between the pins on the squirrel cage at the end of the drum. It would not catch another pin to go on to 2nd. It would catch a pin to go to first but that was it.
A friend with the ability checked and the recall for the 06 Dyna neutral light and false neutral had been performed in 12/05. Upon counsel with him, we decided that the transmission had to come out to check if the shifter drum, shifter forks or detent arm was at fault.
I pulled the bike apart to the point of pulling the main drive sprocket and the inner primary bearing race and took the bike to Cajun HD for this. They charged 1/2 hour labor or $35 to perform this task. A good deal versus $86 for the tool to take the main drive gear nut and $200 for the tool to pull the inner primary bearing race.
I took the bike home and finished pulling the transmission. As soon as I got it out, I moved the shifter drum and the squirrel cage on the end that the shifter ratchet engages to rotate the drum would move without moving the drum. I also pulled it right out of the drum. The splines on the end of the squirrel cage were gone. Now I know why the transmission oil I drained looked like aluminum paint. I called the dealer and they suggested I bring the transmission in and they would inspect it for me at no charge. I did that and they said everything looked fine.
I ordered the drum for $115 and all the gaskets and seals that I could replace for another $75.
I'm waiting on the new shifter drum which has a new part number because the dealer called the motor company and they said that they changed manufacturer. Hopefully the new drum will hold up longer than the original.
Heres the part that failed. The bottom of this aluminum piece should have splines on it. It mates to the remaining half of the steel shifter drum.

 

I got the new shifter drum in and the bike reassembled.
On the test ride, the bike still doesn't want to downshift with one click of the shifter all the time.
It sometimes downshifts and sometimes it takes a couple of tries to make it go down to the next gear.
I am pretty sure that I can hear the shifter drum finish rolling to the next detent just before a successful downshift.
Now, what could be causing the shifter drum to pause before completing the movement to the next detent to allow a downshift? Could it be the movement of the shifter forks that looked fine when I had the transmission out? Or, could it be the dogs sliding on the transmission shafts delaying movement of the shifter drum to completion of a downshift?
I'll be calling the dealer Monday to ask their opinion of what's next.
If it means removing the transmission again, that's no problem now that I am well versed in the removal and reinstallation of the '06 six speed transmission.