From what I know,all you do is the copy the files that come with the res fix to your main SH3 directory,then open the .cfg file and edit the resolutions line,but maybe you already know this and I have misunderstood your question?.As far as I know you dont use JSGME any time for this mod,just manually copy the files to \Ubisoft\SH3
I havent had to run any batch file,all I did was edit the .cfg and load the game and I can clearly see the higher resolution has taken effect
