You're right; I hadn't noticed before: The Mustang and Windstar valve covers are very similar - but not the same.
I took a picture of my old-vs.-new valve covers when I did my isolator bolt fix. Take a look at the 4th picture in this album:
http://community.webshots.com/album/551942761oSNGgS
Hmmm - annoying: My picture didn't quite catch the edge of the baffle where the notch is (but I recall the notch being there).
Your modifications look just right. That's exactly what I'd do.