Most of the mods you've described I've also done. (The only thing missing is ASM compilation.) Basically, I've added complete compilation options. (Within limits of the system.) (I've also made a generic makefile. It compiles all your c & asm files and links them together. Not quite ready to release it, though.)
As far as Make goes, that's the nature of the MinGW make. It interprets /w et al as w:\. I'm pretty sure that the linker will accept -w style flags, but I know for sure mpasm won't. Cygwin won't do this, but interprets \ as an escape character.
I wasn't able to fine Make on the gnuWin website; maybe you could link us?