Disassembly:

1. Drained oil and disconnected negative lead from battery.
2. Removed sump (note that in my case I did not need to remove my exhaust pipes, as they flow nicely around the sump area). This removal was time-consuming because of the location and tightness of some of the sump bolts. Make sure you have a good quality hex key.
3. Removed oil pump. This is a good opportunity to check the oil screen on the bottom. Mine contained some gasket/sylastic material, but not sufficient to worry about. I removed the pump to give me better access underneath.
4. Disconnected clutch cable at left hand side of engine.
5. Loosened footpeg on LHS and rotated it out of the way.
6. Removed shift lever.
7. Removed ignition pickup coils (mine is an E model with electronic ignition) and associated paraphernalia. Disconnected small wire from neutral indicator switch so that coils unit could hang freely.
8. Removed left hand cover. I left all items behind this cover in place. This cover needs to be removed to gain access to the transmission countershaft bearing support housing cover, behind which you will find the suspect 2nd gear.
9. Removed transmission countershaft bearing support housing cover. Can be a bit tight and fiddly, especially as it needs to slide over the shaft normally holding the shift lever. At this stage I was able to see 2nd gear on the counter shaft.
10. Removed the circlip and washer from LHS of counter shaft. These hold 2nd gear in place.
11. A bit of pushing and light tapping from beneath allowed the removal of 2nd gear from the shaft. It caught at the spot where the circlip normally sits, and required some gentle persuasion with a hammer and screwdriver to push it off the shaft. At this point I was able to inspect the dogs on 5th gear facing 2nd gear. They looked rounded to me. Also the slots on 2nd were somewhat worn. The rounded dogs on 5th were rounded horizontally and vertically, thus enabling them to slip out of the 2nd gear slots, hence the problem. An image of this 5th gear and dogs is attached. The extra shiny bits on the image indicate the worn areas. I could not get this image any clearer. At this stage I could not ascertain the condition of the shift fork, and therefore moved to the RHS of the engine to begin some dismantling there. The idea was to remove as much as was necessary to get to the shift fork shaft, which had to slide out of position to enable me to remove a shift fork and hence remove 5th gear.
    
12. Removed RHS footpeg, brake pedal and kick start lever.
13. Removed alternator cover.
14. Removed alternator, by slightly loosening the retaining bolt, and using a pulley-puller to slowly slide the alternator off the tapered shaft. I did this in stages, each time loosening the retaining bolt a bit more, and using the puller, The alternator slides off nicely, whithout damage to threads and such.
15. Removed RHS cover. If this is done carefully, the gasket will remain in good condition. Don't lose the washer on the kickstarter shaft. The clutch had to be removed so that I could continue with my inspection of the shift fork.
16. Removed the bearing housing bracket.
17. Removed small circlip, washer and shim, and large circlip.
18. Removed clutch damper assembly.
19. Removed primary gear and chain.
20. Removed clutch outer housing. Take note of the very large diameter shim.
21. Another washer and circlip came off the shaft in front of the clutch pressure plate.
22. Removed the 6 clutch bolts, pressure plate, clutch discs and plates.
23. Removed washer, and the little rectangular bar that sits cross ways in the shaft. At this stage the ball bearing that sits at the end of the clutch push rod becomes visible. There is no real need to remove it. Just keep it in mind.
24. Removed the clutch nut. For this I purchased a deep plumbers socket size 1 1/4 inch. Clymer says 1 9/32 inch, but the one I bought fits like a glove. I had a spare one of these nuts to test it in the shop. Metric size: 32mm.
    
    I kept the shaft from rotating by welding a small bit of steel rod onto an old metal clutch plate, and then fitting this onto the clutch boss. This bit of welded rod stuck out the side so that it pushed against the case, and hence stopped the shaft from rotating (CBMMA #32767 copyright).
    
    
25. Removed the clutch boss assembly.
26. Removed the E-clip on the forward shift lever.
27. Removed the forward shift lever arm, spring and pawl, to gain access to the end of the shift fork shaft.
28. Removed the E-clip from the shift fork shaft. To do this, you need to be under the engine, looking up. The clip is about half way along this shaft. There is also a washer there. Note the position of the clip in relevation to the washer.
29. Partially slid the shift fork shaft out the right side of the engine. I only slid it sufficiently far enough to remove the shift fork between 2nd and 5th, and to remove 5th gear. I did not see a need to completely remove the shift fork shaft, as I had no intention of removing the entire countershaft.
30. Removed shift fork between 2nd and 5th gears.
31. Removed circlip and washer holding 5th gear in place. Discard this circlip, as it bends too much out of shape during this removal process. A new one here cost me $5 AUS, from Yamaha. At the time of purchase, they had 6 left in the whole country!
32. Removed 5th gear from countershaft, in a similar fashion to the 2nd gear removal, ie out the left hand side of the engine. At this stage I could really inspect the dogs on 5th. They were indeed rounded to the point that they could easily slide out of the slots on 2nd. The shift fork had slight scuff marks on it, but was fortunately not bent. Note that if you remove all shift forks, that you remember which goes where. They are not all the same. I took 2nd and 5th gears to a motor cycle engineer, who took one look at the dogs on 5th and told me they needed to be reshaped. He has since done so (for free, since I did some computer work for him), and he put a slight undercut on the dogs. He did not do anything to the slots on 2nd, claiming that the face hardening would disappear, leading to faster wear on the slots. He ensured that the dogs all contacted the end of the slots simultaneously, i.e., even contact on all three dogs and slots. I re-installed by following the reverse of the above, taking note of suggestions and alignments as oultined in Clymer.

Reinstallation:

1. Replaced 5th gear on to counter shaft.
2. Installed new circlip, and washer.
3. Installed 2nd gear on to counter shaft.
4. Installed washer and circlip.
5. Replace shift fork, by positioning it on 5th gear, and on the shift drum.
6. Slid the shift fork shaft back into position. Don't forget the e-clip on that shaft; it can be a bit fiddly.
7. Replaced the forward shift lever arm, spring and pawl, and e-clip.
8. Temporarily put the gear lever back on the gear shift shaft, to put the bike in 2nd. This is necessary to check the alignment of the forward shift lever and the shift drum. Two marks need to be aligned for correct setup. Mine was slightly out. This alignment is necessary for proper gear shifting.
9. Checked that spacer and flat washer that sit behind the clutch boss assembly were still in place.
10. Installed the clutch boss assembly.
11. Replaced conical washer (convex side out), lockwasher and nut.
12. Tightened the nut using the plumber's tool. I did not have a socket large enough to find on the end, so could not use my torque wrench on it. However, it is tight!
13. Pushed, using a long thin screwdriver, the ball bearing back into place, replaced small rectangular pushbar into the slot on the shaft, and replaced the washer.
14. Replaced all friction plates and clutch discs. This was a good time to inspect the friction plates. Two of mine were pitted badly, so I replaced them with some spares. Aligned all tabs on the friction plates.
15. Installed the pressure plate, and installed only 2 springs and bolt, finger tight. this is necessary in case the alignment of the tabs is not quite right.
16. Slipped clutch outer housing into place for final alignment of tabs. Removed the housing.
17. Installed all other springs and bolts and tightened to 6 ft-lb.
18. Installed circlip and washer.
19. Replaced clutch outer housing, ensuring that large shim was still in place.
20. Replaced primary gear and chain, and clutch damper assembly.
21. Replaced large circlip, shim, flat washer and small circlip. D and 2D models may require an extra circlip here somewhere.
22. Replaced bearing housing bracket.
23. Fitted RHS cover. I used some silastic on the gasket face.
24. Fitted the alternator and alternator cover.
25. Replaced the transmission countershaft bearing support housing cover. Once again was a fiddly job, and quite tight.
26. Fitted LHS cover. Used some silastic on the gasket face. Reconnected clutch cable.
27. Fitted ignition components. This was a good time to inspect the counterweights on the advancer. Replaced ignition cover.
28. Replaced oil pump and screen.
29. Replaced sump. Used LocTite on the bolts, and silastic on the gasket face. Refilled oil.
30. Re-connected battery.
31. Adjusted clutch.

The entire job took me a week, which included waiting for the dogs to be re-cut. The actual dismantling and re-fitting took a day each, working carefully and steadily. Since this job I have had no problems with 2nd gear!

Beers and Gears,
Bill Westerhuis (Down Under).