Looking again today at the gears I can see the dogs on secoundary pinion V have worn/damaged corners. And secoundary pinion I that the dogs go into has damage. Am I right in guessing that pinion V is fith gear, and pinion I is first??
Yes, gear V secondary controls the engagement of gear IV and gear I. Secondary gear IV and secondary gear I freewheel unless gear V engages either of them.
Gear VI on the secondary also controls the engagement of secondary Gear II and Gear III. The III/IV gear on the primary works engages the V gear and the VI gear as well.
If secondary gear V has damage, it wouldn't effect gear II. Pinion VI (and its shift fork) would affect gear II and Gear III. How do those pieces look?
If the bike is in gear III, the shift fork is neutral, meaning no load. In gear III, secondary gear VI engages gear III, and primary gear III/IV is held in it central position.
This doesn't look like the V pinion problem.
As When I got the problem of the horrible clunking, and felt the bike struggling to get in to gear when in third. I had to limp home, but had a few steep little hills to climb which ment I had to go hard in 2nd gear, which was fine. 1st also didn't have a problem, but don't know about fith as didn't want to try to push past 3rd and do more damage. Most of my riding is tight woods stuff so I would hardly ever use fith, mainly 2nd, 3rd, and 4th. So I'm not sure these pinions would cause a problem in 3rd????
Did you look at the mechanism which indexes the shift drum? If the shift drum rotates freely, it can cause the gear selector to move. I'd double check this. Things will clunk, but since the drum is controlling the position of the gears, nothing will bind up. slip, (false neutrals), but not bind. If that spring is bad, or the little wheel that rides on the shift star is bad, or the shift star itself is bad, it might explain what you experienced.
As for the forks, yes they do have wear marks on either side of the flat large surface. Not sure what you mean by the gears putting lateral load on them, or how/why this is a problem?
The fork is designed only to slide the gears so that the dogs can be engaged. The dogs are generally undercut a bit so that they stay engaged under load (the load on the chain actually pulls the gears together). If the undercut is gone, side loads from the gears "push" on the shift forks, putting a lateral load on them. This is how they wear or bend. The only lateral force on the shift forks should be when the fork slides the gear on the splined shaft.
Can't afford to spend loads of cash replacing parts if they are not the problem, but don't want to put it back together and still have the problem.
Another thought i had was the condition of the secondary shaft or the sprocket splines are at. Is it possible that the splines on either the shaft or sprocket are shot? if they are on their way out, it could be symptomatic of what you describe.
without seeing pictures, those are my best guesses. if you can post pictures, that might help a great deal.
Thanks