Yeah, the next step would be to get a 10-yard-fight .nes file onto the ROMS and then see if it works, then you at least know your devcart mods, programmer, etc. is working OK, and the problem is not because of your custom software.
The 29C256 is a flash chip, no? Are you sure all the pins are the same as the mask roms? You may have to lift a single pin or soemthing to disable write mode or that kind of thing. Double check the pinouts.