Hi fj70nz.
A process of elimination I would go about it, some of which you may have done already. I'm not a machanic, but I'm a firm believer in using a big enough, a big enough hammer if it don't move.....so to speak. But here's my 2 pence worth....
I had an issue many years ago with spongy brakes and having to bleed them cause of air in the line. My first port of call was to check for kinks in the line that may have ruptured on the corners of the kink and letting air in, same would go for any tiny pin holes or splits in the piping that may have aged or corroded. Also check where the piping enters and exits certain parts, sometimes threads are x threaded or are not seated 100% correctly.
But saying just that, one would notice fluid leaking out and a drop in fluid level. You would notice maybe eg: clutch slip, leaking or smell/smoke from bellhousing, if it were down the business end of things.
With my issue, I found it out to be a rubber plunger that had perished and got damaged from a small score on the inside of the master slave cylinder. I simpy honed the inside of the barrel and replaced the rubber plunger with a new and put back together and hoped for a good result. Bingo! it worked a treat.
Interestingly you mentioned the master slave cylinder looked in good nick and fairly new. Me just wonders if this may have been an existing problem? If so the master slave cylinder should be good and you need to investigate further down the line towards the clutch end of things
This may not work for your situation, but hey that's my 2 pence worth and hope it may have helped.
I'm interested in the outcome, keep us posted on the progress.
Good luck