Very nice post! As usual, I have a bunch of comments (you should get used to them by now :p ).

Einstein realized in his theory of special relativity that both statements are incorrect: it is not mass nor energy that is conserved, but the sum of both.

This made me jump out of my chair. Energy conservation is a key principle of physics. Energy is conserved. No matter what. At the fundamental level, energy can however exist under three forms: mass energy, kinetic energy and potential energy. And it is the total energy (the sum of the three) that is conserved.

Along the same line, I am feeling very uncomfortable with your spring example. When you discuss this increase in mass, you actually refer to an increase in relativistic mass. This is very a unpopular concept among particle physicists. The reason is that we name it differently: energy (divided by c² but for us c=1). The concept of mass is only used for the intrinsic mass of the system. I actually have troubles to understand why people tend to call 'mass' something that is just the total energy of the system.

For the case of the atom, things are slightly different as we are talking about a closed system whose mass is thus defined by its components (their mass and their interaction). This is a different story from the one of your spring.

Measuring the mass of Quarks directly is unfortunately impossible: quarks cannot be observed unbounded, so it is impossible to determine their rest mass.

A detail: except the top quark as it does not hadronize.

PS: I wrote a couple of posts on neutrino physics months ago, if you are interested ;)