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.