Right- good questions.

First, I think getting a rigorous answer to this 'mystery of pain and pleasure' is contingent upon having a good theory of consciousness. It's really hard to say anything about which patterns in conscious systems lead to pleasure without a clear definition of what our basic ontology is.

Second, I've been calling this "The Important Problem of Consciousness", a riff off Chalmers' distinction between the Easy and Hard problems. I.e., if someone switched my red and green qualia in some fundamental sense it wouldn't matter; if someone switched pain and pleasure, it would.

Third, it seems to me that patternist accounts of consciousness can answer some of your questions, to some degree, just by ruling out consciousness (things can only experience suffering insofar as they're conscious). How to rank each of your examples in severity, however, is... very difficult.