I stripped the gearbox this evening. Generally good condition, with the usual wear on the pinion bushes (I think I will be rebushing them, and the pinion sleeve too). All three shafts mic up correctly and there's no obvious damage to them.
The 3rd/4th selector dog is worn/galled in the groove where the fork runs, and the fork is worn too (around 15-20 thou of wear on the fork at the worst point) The peg in the track of the selector fork is good.
The end float of the gear control shaft I measured at 60 thou with a DTI once I had removed the outer cover.
The end float on the layshaft was excessive too, but I have not measured it (the mention of drilling a hole in the outer bush to measure end float is a good idea, I may well do that)
Someone has definitely been in there before me though. The oil flinger washer which should go between the 1st speed mainshaft fixed pinion and the spacer was found on the outside of the mainshaft bearing, between it and the kickstart ratchet mechanism. It has heavily dished and rubbed against the circlip/snap ring which holds the bearing in the inner cover. As a result the mainshaft has been sitting too far towards the right (by the thickness of said flinger washer) and as such the 3rd speed pinion on the mainshaft was even further from the selector dog. Coupled with the wear on the fork and the excess endfloat on the control shaft it meant that the selector dogs could slide out of mesh as found on my initial peek through the inspection window!
I'm currently waiting on some spares to be delivered, and fingers crossed the selector forks and dogs in the spare box will be a little better than mine. Even if they are not, I think correctly shimming the control shaft, and correctly assembling the mainshaft will solve the problems I have been having.