I have to go to bed, but if anyone wants to get a step closer to compiling it on windows, replace line 173 in ./code/scrypt-jane-portable-x86.h with
#define asm_naked_fn_end(fn) ".att_syntax prefix;\n.def " #fn "; .scl 2; .type 32; .size .-" #fn "; .endef \n" );
The new error complains about _has_cpuid@0 not being defined (in minerd-scrypt-jane.o, after compiling to asm).