You shouldnt have use the water based primer as it may cause the box to swell. But since its already on there you can use enamel spray over top of it (considering it has cured fully already).
It's fine. Let it dry completly before you apply the next layer, and you won't have any problems.
Kiltz is good stuff. I've used it many times. If you go to a paint shop that can mix paints, they can even add color to the kiltz so the base is the right color.