Pretty large space between fourth gear and third gear on the out put shaft Its hard to tell from the angle but it look like circlip #7 is in the groove but with the gap I wonder where and what circlip #13 is and if it is still in the groove. I would give it a complete look over and pictures before you lift the output shaft out to verify the circlips and their locations. I am curious to the splined bushings wish the thrust shoulder on them not like the old style with splined bushings and separate splined thrust washers. it from the views you posted which I would like more I wonder if the third gear slid on the shaft because the circlip #13 might have came out of the groove. And the second gear output #10 shifted towards the dog ring #14 slightly engaging the dogs on them while mean while when you shifted from fourth to fifth the third/fourth gear #12 input shaft that moved over to make fifth gear (by the external dog on dog contact between #12 and #8) anyway third gear on third gear I suspect are always in mesh and only impart drive when the dog rig is engaged. If the circlip #13 came off and the gear moved towards the rear then the third on third might come un-meshed and therefore out of time to re-mesh and well snap. crackle. and grind along with a munching sound. Of course I just woke up and am only on my first cup of coffee. I would like to also know if the nut on the helical gear output shaft is still tight or if it worked loose allowing the shaft to shift with the torque and thrust produce by the helical gear. I will eagerly await your reply Now for another cup of joe so I can think.
Ok coffee in hand and I wanted to mention that while working with a guy 500 miles from me who has a transmission problem. We found or more like Mark found there is a special tool for pulling the input shaft its listed in newer manuals but not the two I have/ Its basically a slap wrench like a dent puller for a car only instead of hooking to the body of the car it goes over the input shaft nose. I am not sure if it threads on to the shaft or if you put it over the shaft and spin the clutch basket nut on the shaft to hold it.
Keep in mind if you have a newer manual my part numbers in the drawing might not be the same I got from my OEM 2006 Manual page 8.19 and page 8.23
I would check all the circlips out to see if they are in their proper grooves before you start pulling the output shaft out. And Once the shaft is out I would verify the circlips are install with correct orientation especially paying attention to any if any came out of the shaft grooves. Noting the condition and if there is any scoring on thrust washers and such.
Go Slow as You do not want to drop and fragments into the crankshaft area. In fact I would try to cover that area even if I had to make a cover plate out of card board to completely cover the crank shaft area.
I really love the ability to study these mechanical problems and solutions from all the member posts. In fact I think I'm addicted to it. But the down side is that I'm starting to develop a paranoia about the integrity of the Rocket transmissions. I realize these are extremes and special cases, but I'm now actually considering selling my 2013 before something major happens. I just love the bike and only have 13,000 miles on it but I'd be so pissed if I got one of these transmission problems before I got say, 75,000 miles. I mean, come on, it's a frigin car on 2 wheels. These tranny's should go 100,000 without any issues whatsoever!
Id would say over all there pretty good and remember I am just guessing from pictorial views and spare parts I have laying around to look at. So that being said we shall hopefully see if I am close once he looks further into it. One thing for sure is once the teeth fragment a few get stuck in between other teeth which gets destructive.
I am just fixated on the large gap between fourth and third gears on the output shaft.
While we are on the tranny subject what does it mean when sometimes my bike is hard to get into first. I have to click down multiple times before it goes in. Not all the time either.