The easy way is to use acetone to remove the old paint. If it's anything less tough than epoxy, it will wipe away pretty easily. Just wear latex gloves while you work unless you want to spend a lot of time and more acetone getting paint off your hands. If the acetone won't dissolve it, you have no worries at all with spraying the new primer over it.

As for worrying about making it fuel proof, it's not a concern for a cowl. I did a glow Cub cowl in yellow Rustoleum and Rustoleum enamel primer (definitely not fuel proof) and it hasn't had a drop of fuel touch it. Still looks good after a year. Unless you're really sloppy with fueling your engine, your cowl just isn't going to get any fuel on it.