After building the adapter (see project details) I was able to run side-by-side tests against an original NES controller and a knockoff brand.  I found that a while both controllers produces accurate results, only the original controller functioned on 3.3v.  This is pretty big seeing as how using the original board mean that I would have much less space.  So, if I'm going to use the original controller, I'm all in - original board an all.  Next up, test out my adapter and the unmodified controllers with an ATtiny85 and see if I can make some noise.