Clutch cable isn't going to make it pop out of gear. BTW WD40 isn't a lubricant, its a water dispersant so I'd probably get something more suited to the job in there regardless.

You've posted in the RS Turbo forum rather than Sierra, but its probably worth stating exactly what oil you've put in there as I know these boxes can be fussy. When was the oil last changed? Putting a flush through it may well have shifted something somewhere you don't want it to be. Either way, with that mileage you're lucky that its only just starting to show signs of wear. Coming from a Ford BC Gbox owner, anything you don't need to change monthly is a blessing