interesting that we have VERY similar problems...
I recently did a complete refresh/rebuild of my 954 engine top to bottom, including fixing a 3rd to 4th to 5th shifting problem (lots of false neutrals, then eventually 4th kept popping in and out).
So, first off I just replaced all the bearings in the gear box along with 3rd and 4th input/output cogs and all three shift forks - worked fine for about 600Kms on the track before the same problem showed up again. We found lots of wrecked dogs on gears, a bent right shift fork, and a damaged shift shaft on the arm at the point where it contacts the shift drum.
So then I replaced 2nd, 3rd, 4th, 5th, input/output cogs and 6th on the output shaft only, along with all the thurst and splined washers, the right shift fork, the shift shaft and shift drum - again all good for around 6-700Kms on the track before I couldn't select 4th under full power (I have a DQS fitted too), but could go up and down through the box riding around in the pits (though it was quite notchy).
This time we went in from the side and up through the sump, to find the new shift shaft was bent where it contacted the shift drum and the right shift fork stuffed - I've decided to replace the selector drum and bearing as well this time around as it's pretty much the only thing I haven't done yet that "might" have some impact on the problem - the Haynes manual suggests that for symptoms of the gear lever not returning and an inability to select a given gear that the selector drum should be replaced. Like you, I could see some light wear in the track for the right shift fork but it hardly looked like anything to worry about...
So, if we don't get it sorted this time around - who knows where to go next ?
Short of dropping the engine and simply replacing everything in the transmission again I really don't know where to go next if this final fix doesn't work.
I should have the bike back on the track within the next couple of weeks - I'll keep you posted.