For those of you struggling to compile this, you actually need to rename the BS F-Zero Grand Prix ROM to "F-Zero_GP2.sfc", and place both ROMs in the F-Zero_Final folder before running the batch file.
I can confirm that Final is running on SNES9x just fine.
I would also like to note that the current build is unable to display the Ace League on the Records screen; will there be an overhaul to allow for more than three leagues to be displayed onscreen?