Flying a homebuilt from the US into Canada I believe is allowed, as our requirements are basically the same as the FARS for this category of aircraft. I am not involved with amateur built aircraft, but I have seen RV4's and Cirrus's on the ramp with "N" numbers.
As far as passports to cross the border, the first answer that comes to mind is "yes", if anything to make it easier. But I believe that photo ID and proof of cititizenship is also acceptable, but I think a passport is the preferred form of ID. The days of having only a drivers license as proof of who a person is are gone. Everyone that I work with have their passports, just in case we ever have to head south on a quick trip.
John
