You're asking some pretty loaded questions. I still really think to get the right assistance we need to see what you're working with. It sounds more and more like you're dealing with something beyond simple technical support, but I can't tell at all what you do or don't have. Please show us what you've got.
You're not going to be able to use a controller. A 357 is NOT just a PS3, and the software on it isn't going to just plug and play a controller. The game is designed specifically to interact with the USBIO in the cabinet.
This whole time I was under the assumption you have a cabinet. This is why I've been asking.
There is literally nothing I can do for you man, these are intended to work in a machine. It might be a bit forward, but I'm 99% sure nobody is going to get that working for you. A waste of time to try, sorry.
The problem is it's not just a JVS game or anything, and the IO board isn't an easy replacement to get, unless anything changed. You're not going to get anyone to hack this for home use otherwise, it's not happening. PS3-based stuff isn't a breeze to work on like PC-based hardwares. There's a huge number of issues to tackle, it's just not worth it. You're better playing the Switch version or finding a crack for Nijiiro
EDIT: Note also the 357 for Taiko doesn't have the JVS board, so it's useless for almost anything home use really. I bought a stack of them before I realized this, they are pretty much paperweights to me atm
Do you think dumping it and doing research myself I could try to get it to work? Or finding someone else to read through it and change things? That is my best idea for now. Hit me up for any more ideas though.