Ok, I'll be honest. After reading everything up to now I still have 0 idea of whether this is malware or not. If there's a line implemented there which affects your hardware. That can be easily solved.
But if you would ask me about the card system, I would put a bet that it isn't our biggest problem regarding FGO Arcade. I think a bigger issue in here would probably be the payment. As far as I saw, You need to use an arcade card which is charged with money. And regarding the controls, If there's access to the game's script then it's indeed possible rather:
1. Rebuild the entire control panel (Bad idea)
2. Use an external software to reconfigure the keys in the keyboard to the ones that are defined in the code.
But I don't have as much experience in emulating games, Henceforth It's hard for me to actually imagine how it would run without running into issues. But I believe the challenges here lie more in the Practical side then the gameplay side.
ZX3000GT1, If you can confirm or give me at least a thought that it isn't malware. I'll get the file, Download it on my second pc and see what may be possible to do on it. But if it's still malware then, Well I guess it's an "Oh well"
-Skipper