Rob,
No, I am afraid not. There are issues with paths on most of these makefiles. But the most common problem is the included files or defines for the compiled file is not found.
I did manage to get the cores compiled. There again it was a path issue on the version I used. Yours however had the path correct but could not find a rule to compile for adruino_pins.o. Which means it could not see the file, I think.
I will use a smaller project to test on today. I am sure that there must be something small with the windows setup. Once I have made some sense (i hope ) of it all, I will give some feedback. I will be taking a small break soon so it might be a week or so from now.