Jeff:
Most AN hardware is electroplated with cadmium and dichromate, the latter giving it the gold color. This coating has excellent corrosion resistance, and is likely even better than bare alclad sheet. If you end up priming components as many builders do, the fasteners get the benefit of this coating as well. Some AN fasteners, such as prop bolts, spar fasteners, etc. are "graded" for strength and must NOT be replaced by stainless. Grade markings can be found on the head of the bolts.
Your choice on priming (many threads on this subject), but my own choice was to alodine and zinc chromate prime any bare (un- clad) aluminum and to lay down primer on the contact surfaces between joined parts. This was easily done with zinc chromate in a rattle can. My approach to corrosion resistance was taken after conducting a series of lab tests using a certified salt spray cabinet and testing to ASTM standards.
Back to your original question, I would not replace any of the AN fasteners that come with your kit. You might however, consider aftermarket wheel fairing attachment brackets made of stainless. Much stronger than the aluminum standards and highly resistant to abrasion and corrosion. Also, braided stainless brake lines in the cockpit aren't a bad idea.
Have fun. Good luck in your adventure.
Terry
RV9A
N323TP