It sounds like a much better, and easier, solution would be to use one of the so called NOAC (NES-On-A-Chip) devices that they sell online and in various catalogs. These are single chip boards that completely emulate the NES, many of which still have the traces to connect a cartridge slot to it.
Pairing one of these with a collection of NES ROMs (I know there are some re-writable NES cartridges out there, but I don't know the price point) should prove to be much easier developing a whole mini-distribution just for running an NES emulator (besides which, I have found most emulators for Linux to be lacking anyway).
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