Your misunderstanding is an amalgamation of multiple misconceptions perpetuated in science education media.
- Forces are caused by exchanging particles
- The quantum vacuum has things popping in an out of existence
- cartoons of nuclei with distinctly colored protons and neutrons
3b) Atomic orbitals have electrons randomly zipping around and if you measure its position it will have probability of being here or there.
1: So yes, perturbative calculations involve the exchange of virtual particles, but they're just approximations to what's really happening: the field configuration follows the Feynman path integral formulation, which we can't calculate analytically, nor really visualize.
2: The vacuum doesn't change. It's invariant under space and time translations, and between one observation and the next, it takes all possible paths (per (1)). There is an old fashioned way to calculate that where particles pop in and out of existence, violating energy conservation per the uncertainty principle, but that was superseded in 1948 by relativistic quantum field theory. The vacuum just is, and it's not nothing.
Note that particles popping in and out of existence is clearly not invariant under boosts, e.g: what is the average momentum? Which was does it point? Is it zero in all frames? it's just not a relativistic way of thinking: it has to be frame dependent.
3: A stable nucleus is the ground state of a many body quantum system. It is an energy eigenstate, and thus a stationary state: it does not change. For instance: all alpha particle are identical, everywhere, and always. Nevertheless, you can use the effective field theory of meson exchange to calculate properties. It does not mean they are a boiling froth pion exchange in real life. Likewise for 3b, though atoms are simpler since we can treat them perturbatively.
3: The nucleons in a nucleus do not have distinguishable proton and neutron identities. For instance, a deuteron has the hadronic content:
$$ \frac 1 {\sqrt 2} \big(|pn\rangle - |np\rangle\big) $$
So, each nucleon is not in an isospin ($I_3=\pm \frac 1 2$) eigenstate, but together they form an eigenstate of total $I_3=0$. The math is isomorphic to angular momentum, which is why it's called isospin .
So, in summary: don't take virtual particles too seriously, and don't take classical descriptions of quantum systems too seriously. They are both helpful in understanding, but can generate more misunderstanding if taken literally.