1) Are you using metric feeler gauges because I can't see the engine running with .002mm clearance when it's supposed to have .1mm? Please verify that your clearance is supposed to be .1mm because I don't have your service manual...
Using a .002inch feeler gauge would give you .05mm which is half what it is supposed to be. If you only have feeler gauges in inches - then use .004inch.
2) Are you aligning the T mark on the crank and then the timing marks under the valve cover? You may be trying to check the clearance on the wrong stroke.
What you are describing is not normal, I think you need to check your procedure and your feeler gauges because with a gap of .002mm the engine would not run.