With stock everything (including longbranch manifolds) and the original starter, I've had the hot starter issue for as long as I can remember. It happens when the car sits for about 5-10 minutes after running. Sit much longer and the starter cools down sufficiently to work normally, sit less and the starter doesn't have time to get hot enough to bog down. Since the engine is warmed up, it always starts OK with even the slightest cranking but that has not taken away from the anxiety every time the starter is obviously struggling.
It happens on gas fill-ups, the quick run into a store for something, etc. I've learned to not trust shutting the car down for a freight train or long traffic backup.... just in case. Wouldn't want to wait for the thing to cool down while in the middle of the road.