I have yet to find a principle within quantum mechanics to be counterintuitive. Your understanding of the rearranging of particles, however, is atrocious. The rearranging of particles does not take place on the scale on which you are describing. A set of particles cannot, out of nowhere, create the macroscopic structures which you are positing that they can. These rearrangements take place on the quantum level. What you are positing, are that things such as nuclear rearrangement which take place within the electron, are capable of forming large scale, physical structures at a whim, and that is simply not the case.
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