yeah you're supposed to have that shit done by a machine shop so its flat and checked for being true. Most flywheels are stepped, so you have to machine both levels of surface sometimes so that you have the proper spacing. If you machined it too far (and it sounds like it), then you will have issues with the clutch engaging - you won't get the full clamp load, and with a cheap clutch that likely doesn't have much to begin with (not to mention purely organic friction material). And if you had hot spots or worse, cracks, then it absolutely should have had the flywheel turned by a machine shop.