360 F1 pump

My brother has a concern with the F1 pump. The car, an '02, started popping out of 6th gear after 30 or 40 miles, so he had the clutch replaced (turned out it didn't need it -- very little wear -- but once you're there...). Anyway, the shop also put in a new relay, per posts here, and ran the setup routine with the diagnostic computer. Since then everything has been working fine. The only worry now is that the pump runs a long time, 12 to 15 seconds, when you open the driver’s door after the car has been sitting overnight. Thought it might be air in the system and tried bleeding the clutch. There was no sign of air in the fluid and the pump still runs an unusually long time. Thoughts? Thanks!