If you put a new flywheel in, did you replace the pilot shaft bushing? When you pushed the clutch pedal in, it releases the clutch inside, and if the pilot shaft bushing is bad, it will make a grinding noise.
As far as the shims, loosen the top bolt on the starter, and take the bottom bolt out, tilt the starter a little and slide the shim or shims in, it shouldnt take 1 or 2 to be lined up. You will know if its lined up by tightening everything up and trying to start it, if it engages quietly, then its in line, if it sounds like its chewing on the flywheel, install another shim. I think they come in a 3 pack. Only a few dollars.