Ok, when you downloaded NitePR inside the main folder there is a file called "NitePRed.exe" copy this file and "nitepr.prx" from the Files>ALL OTHER FIRMWARES folder to your desktop. If you need NitePR download it here
Run nitePRed.exe, read the warning and press enter. Now type in "3" and press enter. Follow the onscreen instructions to change the buttons. I'm booted into ubuntu so I can't run it to give you more detailed instructions just follow what it says to change the buttons it should be pretty straight forward. then just save and copy the nitepr.prx on your desktop to ms0:/Seplugins/.
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