That's going to be a seriously nice boat to spend a day on the water in, bet you're going to be real happy with it. I absolutely love my Merlin. Ya done good on choice of designs!
Internal or external stems is a religious argument, just as is staples-vs-no staples and cove-and-bead-vs-rolling bevels. Study your options, then go with what you're most comfortable with.
I skip internal stems because I want to save weight wherever I can, and because I'm confident the finished boat will be plenty strong without 'em. I always add external stems, however, almost purely for cosmetic reasons. I want my boats to look good, and damn good will be even better. Still, they are generally considered to be a sacrificial wear strip, but I've never had to replace one.
You can use strips of any width and thickness within reason, but you'll save a lot of corrective work if you ensure they are consistent. I've been openly and expressly accused of suggesting micrometers here on this board, and can never understand it. BS! What I suggest is taking one strip that's cut to the size you want, then bless it as sacred and holy and protect it from all harm, and use it to set your fence each and every time you cut strips from here on out (I have 6 "master strips" that are roughly 9" long, keep 'em in my tool locker, have had 'em for years). That simple procedure works wonders keeping output very consistent, and save lots of tedious fixit time. Also, take your time lining up strips while the glue's WET; minutes doing so will be paid back in hours of time saved sanding out the uneveness after the glue has cured.
If you want to go staple-less, then go for it indeed! I use staples, but have a friend who doesn't, and amazingly enough comes very near to keeping pace with me in building speed. I've often thought about going staple-less myself, but have little incentive since I actually rather like the look of the faint rows of staple holes.
I almost never use one-by lumber because I almost can never find any that's clear enough (knot-free). Seems I have much better luck picking up 2x4's, 2x6's, 4x4's, 4x6's, etc., and milling them into strips. Now that I'm in the habit of passing up the one-by stuff without even looking at it, I have the added benefit of never having to sweat strip widths because a board was planed too thin at the yard or whatever. Also eliminates rough edge syndrome. It's actually EASIER to mill consistent strips when you use a well thought out procedure up front, as is true in most routine woodshop tasks (I've made my living in a woodshop once or twice).
Bead and cove works better on canoes than anything because canoes are so completely curvy. If it's ever going to be appropriate, this would be where. Kayaks have lots more flat surface areas to strip where no edge treatment is necessary. Barditch is right: we generally poo-poo B&C here, but even still, it's a religious argument, and your mileage may vary.