You don't have to put registration numbers on your canoe when registering it in Minnesota (people tend not to believe me about this, so I refer you to page 6 of Minnesota's current rule book). All you need is Minnesota's registration decal. Also, the boat just needs to be registered *somewhere*. It doesn't have to be registered in Minnesota, so that leaves you the option of registering it in your own state instead.
I understand the gripe about paying for registration, but saving a mere $8 per year wouldn't be enough to make me choose a design that performs poorly ($8/year is 15 cents per week, which is less than you can pick up off the sidewalk on any given day). I know it's the principle of the thing, but at least be aware of the registration options above.
I'm not a boat designer by any stretch of the imagination, but I'm thinking that for rough lakes you might consider one with a hull that is rather rounded in cross section. As my screen name implies, one of my double-ended rowboats is an Adirondack guide-boat, who's profile as seen from one end is very rounded and broadly flared. The boat's "footprint" in the water is a lot narrower than its overall width. I routinely take that boat out in waters far more rough than what I or most people would do with a solo canoe (though much of the trouble in a solo canoe at those times is the strong wind, something that a rowboat handles with comparative ease). Even with a height amidships of only 12 inches, this is by far the driest open boat I've ever used. Some of the reason that boat feels secure in big waves is the low seating position (about five or six inches off the bottom, I think), but a lot of it is the rounded hull. A rounded hull profile means the hull is not all that stable "as it sits there" (people usually call this primary stability), but it also means that the water can tilt beneath it and it doesn't get rocked back and forth. As far as the seating arrangement goes in rough water, I'm not sure a high seating position would work so well in a canoe, but kneeling certainly would.
My other double-ended rowboat is smaller than the guide-boat, with a most peculiar bottom profile having reverse curvature each side of center, creating a sharp chine on each edge. It's not designed to have low primary stability like the guide-boat, but the primary stability is low on account of the overall small size of the hull and the fact that (for someone of my weight) it's easy to lift one chine completely out of the water, so it also does quite well in chop.
Pictures showing the hull profile of these boats would not be hard to find online.
One of my canoes (Novacraft Supernova) has a bottom profile that's quite rounded, and though I've only used it as a tripping boat on rivers and for whitewater, I think it would do well in rough waves on a lake, if not for the fact that it's also my least wind-friendly canoe (I probably never will try it in big lake waves on account of the wind issue, at least not intentionally).
If not in rough water, a rounded hull profile (and narrower "footprint") would still be faster and more efficient, but it sounds like that would not be a design goal for you.
I had one final thought on width. My double-ended rowboats are very wide, I believe the guide-boat is 38 inches and the small boat is 36 inches across at the widest point (width of the hull itself, minus the gunwales would be a couple inches less). At that width, solo paddling either boat with a single-blade paddle would be out of the question. Do you use a double-blade paddle or a single? A double-blade would make paddling such a wide boat do-able. If you are a single-blade paddler, I still agree with those who've suggested you try a really wide solo canoe before building one.
extra wide 13’ canoe I had one of those. Just to back up what GBG said, width doesn’t necessarily = stability on rough water. My 14’ x 28" solo canoe with shallow arch bottom is far more comfortable on wind waves than that 13’ x 39" with flat bottom.
At the risk of being redundant, I also agree that at under 9’ you’d have much better performance rowing a guide boat or “Whitehall” style.
paddle I generally paddle alone with a double blade.
I have a small 11 ft X24 inch solo canoe but have to sit flat on the floor to keep it upright. It is very fast though and will go as fast as I can crank the paddle.
Stability In case you are unaware stability increases as a cube of the width(all else being equal) so your proposed 35 inch wide canoe will have more than three times the stability of a 24 inch so it may be a bit of overkill.
With regards to speed you should easily reach “hull speed” in a 9 ft canoe so I would suggest a prismatic coefficient around 0.65 to give a higher top speed.