Well, I ended up sanding the keel down, grinding out the cracks with a Dremel and fairing with Watertight. After that I added four coats of 2000E and then the bottom paint. I found it a little difficult to get a smooth application of the 2000E, I think I'd use a different roller next time. The foam roller I used left a bit of a texture behind.
While I was at it, I did pretty much the same thing to the rudder which ended up being a good thing. While sanding the paint off, a few inches of gelcoat chipped off the leading edge of the rudder, revleaing voids in the original lay-up, I filled them with Epoxy, then covered the rudder with four coats of 2000E and bottom paint.
We shall see how it all looks in the Fall.
-Jeff