Could you please link to a review or other material that documents the clear science that "some people are stuck with bodies that are a different sex from what they actually are"?

I assume that you mean the sex that someone "actually is" is the sex of their brain, assuming that this is a thing.

This is a different claim than that gender dysphoria is a real thing because, for instance, you can imagine an individual who has a female body and a female brain (to the extent that there is such a thing) except for one difference which is that the brain tells the person that they're supposed to be a man. Alternatively, you can imagine an individual who has a female body and a male brain (to the extent that there is such a thing) and the male brain does all its normal things including signaling to the person that they're supposed to be a man. Either way, you have gender dysphoria.

Gender dysphoria is clearly documented--no need to reference that. Can you reference what you're claiming?

(This must have two parts: first, a demonstration that male and female brains can be very reliably distinguished somehow; and secondly, that this reliable measure indicates that in at least some trans people, their brain-gender is the gender they think, and at a frequency that is far too large to be explained by measurement error.)

I also don't dispute that there are some indications that this may be the case--you needn't link anything merely suggestive. Your claim is that the science is clear, and the great thing about clear science is it's really easy to show and get everyone else clear too, because the evidence is presented!