Clearcoat on engine

I don't think I'd clear it- I was always under the impression that engine enamels needed to go through a number of heat cycles to fully cure and toughen them up; and clearcoating may prevent that ("outgassing" if that applies here?). Maybe I'm mistaken- its not like that's never happened before. :)
I'd just touch up your boo boos with paint and a Q-tip and run it.