It's the master bleeding pressure out into itself. This has been discussed so many times on M.net. If your slave isn't leaking and you have trouble getting into gear despite having changed the clutch pedal adjustment, then it is the master cylinder seals that are leaking. There are two seals. One keeps fluid from coming out of the back of the master cylinder and leaking into your carpet through the firewall. The other is farther in the shaft whereby fluid pressure gets forced back into the reservoir. You can check for a wet carpet but that probably isn't the case since you've spent so much time in there already. Check for a rise in fluid when the clutch pedal is depressed and there's your fault.

 

Can you get rebuild kits for the master, or is it a case of having to buy completely new?

FWIW in the last few days I swear it's been getting better - or maybe I'm getting used to it. Still every so often you can feel the dog gears semi-clashing and the box clunking into gear, no grinding, just clunking.