If your custard comes out pockmarked with holes, your oven might be hotter than you think it is. The higher heat creates air bubbles in the custard. But you're in good company. This is very common in restaurants when they're trying to produce the dessert on short notice. And, no, it's not a good idea to try to cook custard in a microwave.
Custards require a slow, steady heat source.
Surges of energy cause uneven cooking and holes in your custard. It's in the recipe to guard against potential crystallization of the sugar. Without the corn syrup, simply be more careful when cooking the sugar. Remember to start with clean sides in the pan. Always partially cover the cooking caramel.