Good to see you read the whole post
Already changed gearbox oil and added molyslip, and suggesting a new slave cylinder & braided lines will not help it being notchy when cold
I think Wills point with these is that it usually fixes the floppy pedal issue that the OP is having also. But, those items have also recently been changed and so are not the issue.
I think the floppy pedal is because of the pedal adjustment, if by that you mean you adjusted the pedal to sit lower. It's common for this "issue" after the adjustment and it's the same in my car, but doesn't cause any problems so I haven't bothered fiddling with it.
As for the main problem here, I have no idea. Usually when this issue arrises, changing the fluid and adding molyslip cures it, so I'd go with Alex's suggestion about air and maybe get it bled at a garage?