Shader model 5 semantics
Your best bet is, as you say, to pass these values as secondary semantics (i.e. pass both a "POSITION" and a "SV_POSITION" value). Note that if you place SV_POSITION at the end of the output declaration for the vertex shader, you may omit it from the input declaration for the pixel shader.
Regarding the internal error, this is typically due to the declaration of a texture or other shader input that is optimized out in one pass but not in another. Disabling optimization typically works around the issue, but you should also be able to fix it by eliminating unused (including via dead-code elimination) input declarations, and ensuring you avoid complicated code that reduces to no-op.
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