Never use epoxy unless you want to make it a mess.
Plug the holes with a rag, and thoroughly scrub the mating surface with a soft bristle brass brush. If doesn't clean enough use a higher number emery paper wrapped around a small and straight piece of wood for a smooth and even finish.
Don't leave scratch marks!
Inspect the O-ring that comes with the pump, it should be soft and clean, evenly tight all the bolts as per recommended torque specs. It should not leak again.
Further, it is recommended to also inspect the metallic coolant pipe connecting the pump and thermostat housing, the condition of the pump housing indicates that the above mentioned pipe may also be in a bad shape.
Once you succeed in stopping all leaks, immediately replace plain water with proper coolant.
Tip:
(Colored) Coolant can help you in tracing tiny leakage areas.