Just to clear things up; the thud occurs when you first start the engine due to the RPM's dropping to about 400-500rpm for a quick second then shoots back up to the normal 900-1000rpm. It's just a small shudder due to the rapid drop in RPM. From my understanding, this is because of the MAP sensor in our cars. You can try giving it the "MAP whack" fix which is simply taking a screw driver and hitting it once or twice. This seems to fix it for awhile. I rarely have this problem; usually occurs when the car is fully warm when starting which would make sense because on a cold start the RPM is around 2000 vs 1000rpm when the engine is already at operating temperatures.

As for the thud/vibrations when turning the engine off; this is primarily because of the very high compression ratio on our engines. All of the moving parts coming to a sudden stop causes the vibration. The fix for this one is simple, hold your clutch in while you turn the engine off and you'll notice it's not nearly as bad at all.
-Tyler