Higher seat for sure for a wider beam. That's the ticket. Get up as high as you can, even if your wife needs to sit lower. that should help. She probably has less beam, and with the canoe paddle has less trouble with beam and freeboard. She still needs a comfortable seat though.

Kayak paddle for the engine room and a canoe paddle up forward is a good way to go. For some reason the woman up front works best, for canoes, kayaks, bicycles, whatever. Not sure why. Pretty to look at I guess.