I think I could try the lapping process, as you said is worth an extra hour or two of work to check the condition. This must be done with a new and fresh flywheel or could I use the actual one? I don't have it in hand but judging by the photos I have seems like the inner taper is also a bit rough.
Researching this topic I found some mention of elongated rods at the clutch slave cylinder to be able to push the clutch further to work. Now I remember that the push rod on my car has some weld added, so seems like something happened there, maybe the flywheel could be already a bit recessed into the crankshaft from previous rebuilds, hard to know for sure right now.
Before the fault the gearbox was working mostly fine, I'm not experienced in this car, it was hard to change from 3rd to 2nd, but with a double clutch, it was fine. I don't think it was rubbing the C clip, but can't be sure it won't with a new flywheel. I have seen that some mechanics increase the recess at the flywheel from new just to avoid any possible contact with the C clip.
This is a mess, but I'm learning a lot.