my understanding is that while there are some candidates from the theory of unbreakability of cryptography and random number generators [eg some cited in Razborov/Rudich, Natural Proofs], most aspects of your question are acknowledged as basically key "still open" questions by experts in the field. from the introduction to the comprehensive survey, Average Case Complexity by Bogdanov and Trevisan (2006) has some related points. Trevisan's youtube lecture on findings and open questions of average case complexity may also be helpful.
Applying the theory to natural
distributional problems remain an outstanding open question.
...
A major open question is whether the existence of hard-on-average
problems in NP can be based on the P$\neq$NP assumption or on related
worst-case assumptions. We review negative results showing that certain
proof techniques cannot prove such a result.
...
In particular, a long-standing open question is whether it is possible
to base the existence of one-way functions on the P$\neq$NP assumption,
or related ones (such as NP-complete problems not allowing polynomial
size circuits).
...
The right techniques to apply such a theory to natural problems and
distributions have not been discovered yet. From this point of view, the
current state of the theory of average-case complexity in NP is similar
to the state of the theory of inapproximability of NP optimization
problems before the PCP Theorem.