I have seen a few Genuine clutches with problems, seems to be something to do with the pressure plate not lifting evenly, causes difficult gear selection and/or juddering. We had one a couple of weeks ago in one of our vehicles, fitted new clutch, you could hardly get the damn thing into gear, took it out for a look, seemed OK, refitted it, same thing, fitted another new one and it was fine. Nothing visibly wrong with any of the components. The bloke doing it was mightily P&ed off taking the box out 3 times in 2 days!!! I guess I have seen 3 or 4 like this in about 6 years so it isn't common but does happen.
The Td5 flywheels should all have been done a long time ago. Unless it was coincidence I don't think a new clutch could cause anything untoward with the flywheel and in any case the cracking problem was only supposed to affect a handful of vehicles that would have a really hard life towing or off road, most vehicles were fine.