FWIW generally the wiring isn't related to the 'board', its just an abstraction to the wiring for the type of EPROM you're likely going to use to replace the original ROMs. Anyway, what kind of chips did you use? Does the rom work properly in a more accurate emulator such as nestopia? A picture of what you're seeing would be nice.
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currently translating Legend of the River King for Famicom