Right! Sounds like there are two issues here. Hard shifting is 99.9% clutch related, most obvious with the nasty clunk you get when engaging first from neutral. It can be sticky friction plates, warped friction plates, warped clutch plates, bad springs or any combination of these. What happens is that the clutch drags, puts pressure on the gearbox, and makes it hard to rotate the gear shifter drum. Plenty of advice on the forum on how to deal with the clutch.
If you cannot get second under any circumstances, it's a gearbox problem (so you did right to tear it apart!). MCRider points out you need to look at the middle gearbox fork, and this is a common issue. I had this problem in the dawn of time, on a 30k mile bike, but it was pretty obvious. Started in the morning, drove quietly up the hill to the road in second, and it started going clack clack from the gearbox, and I could feel the jerkiness as the dogs popped in and out of second gear. Basically I parked the bike and pulled the motor. I replaced the fork only, and rode the bike for another 25k hard miles with no problems. But, like MCRider says, it's a serious downer if you replace the fork and the problem doesn't go away.
Rambling aside, what can you do? The manual is useless, unless you have access to several thousand bucks worth of micrometers, and the budget to back up the measurements. The illustrations can be useful though. It's a freebie to do a thorough inspection of the gears, forks and shifter drum. Check the gears for any damaged teeth. They should all be OK. Check the dogs (round bits that grab into neibouring gears) for damage or rounded edges. The edges will more than likely be rounded, but it's hard to say from a distance how much is acceptable. Rotate the shifter drum and get a feel of how it works. Push the shifter forks back and forth to get a feel of how much play there is. Make a qualified judgement from there (now there's a disclaimer
).
