Qualia has strong features of a confused concept

I submit that it is (many of) the theories and arguments that are confused, not the concept. The concept has some semantic vagueness, but that's not necessarily fatal (compare "heap").

History of science strongly suggests a functionalism under which a version of me implemented on a different substrate but structurally identical should experience qualia which are the same

If "structurally identical" applies at the level of algorithms - see thesis #5 and "consistent position" #2 in this post by dfranke - then I agree.

It feels to me like qualia is used in an epiphenomenal way.

That happens when people embrace some of the confused theories. Then comes the attack of the p-zombies.

I'm all in favor of talking openly about qualia, because that is the hard problem fueling the bad metaphysics, not access consciousness. Self-consciousness can also be tricky, but in good part because it aggravates qualia problems. But I don't think the hard problem is an inescapable quagmire. Instead, the intersection of self-reference (with all its "paradoxes") and the appearance/reality distinction creates some unique conditions, in which many of our generally-applicable epistemic models and causal reasoning patterns fail. If you've got time for a book, I recommend Jenann Ismael's The Situated Self, which in spots could have been better written, but is well worth the effort. This paper covers a lot, too.

(e.g. converging on a theory like that red is to do with wavelengths of light within a mature theory of electromagnetism)

That's the reality side of redness; what people puzzle over is the relations between appearances (e.g. inverted spectrum worries). Maybe I misunderstand you. My claim is that the fact that appearances are mere appearances definitely does contribute to the hardness of the hard problem.

I don't think qualia and consciousness are fundamental in any of the usual senses - like basic particles? And I have no idea how simple and elegant an Essence has to be before it becomes Platonic. But humans think in prototypes and metaphors, and we get along just fine. We don't need to have an answer to every conceivable edge-case in order to make productive use of a concept. Nor do we need such precision even to see, in rough outline, how the referents of the concept, in the cases that interest us, would be tractable using our best scientific theories.