Definitely don't go thinner than 3/4". I used Doug Fir on my last kayak and it was very split-prone (It actually came from a remodel of my 1887 home). If you are thinner than 3/4 you will likely break mortises when you're bending in your ribs. Even with 3/4" stock be sure to clamp on backers on either side of your mortise for the rib you're bending in.

As for the height- I think it's going to depend on your design and how your ribs and deck beams are going to line up. If you build traditionally you'll likely have a lot of both, so you'll definitely have overlap between rib mortises and deck beam mortises. You can do half-blind deck beam mortises or reduce the number of deck beams, but I don't think you want to overlap them with shorter stock, even if Doug Fir is tougher, because it is so split-prone. You won't be building in as much stress with a bidarka as you would building a West Greenland kayak with tons of sheer, but there will still be a lot of stress, and that could make splits more likely.

When I was building it I remember thinking to myself that I'd never use Douglas Fir again, but... that was almost 2 years ago. I'd definitely do it again...

m