Ought to work, but I haven't ever tried it on a PWC. I've done plenty of fly fishing out of various other boats, canoes, and kayaks. Keeping your stripped line from snagging on stuff is usually the biggest issue. The higher off the water to a point is better too. I never liked casting much sitting low in a kayak, but on a PWC you sit much higher with your legs under you.
You could bring along a stripping basket to contain the line. I don't like those baskets much, but lots of people do. I like shorter than the sort of standard 9' foot fly rod on standing and casting in my kayak and I think something 7.5 or 8 feet might be easier to manage on a PWC. There are several salt water weight type fly rods in that length to consider.