I had similar issue with one of my 996 C4S's after purchase years ago - Was confirmed that flywheel had particle buildup and replaced it - Worked smooth after replacement.

 

OK, so talked to my indy this morning. His best guess is that the clutch was abused a bit by the prior owner and most likely the problem is in the flywheel. That surprised me a bit since I was figuring pressure plate more than anything. He is generally reliable as his shop is almost exclusively Porsches and he has seen it all over the years. Also, as I explained to him, I would describe the pedal pressure as firm, definitely stiffer than my 996 with a new clutch, but I wouldn't call it hard. The problem with this job is that barring something on the outside, such as the slave, the only way to know is to actually look at it.

 

Sounds like it’s time to open it up and take a look. You seem to have a good shop!