The motor housing can run really hot especially when in direct sun. This question came up a while back and I think I measured my casing at 140+ and it's inside a poolhouse in the shade. PVC melts below the water boiling point so I'm not surprised it looked burned. Probably a shade of brown. As for starting-stopping vs continuously running, it doesn't make any significant difference in my opinion. Others may disagree but consider motors for refrigerator and air conditioner compressors, shop air compressors, and other motors that cycle often. They last for many many years typically. The noise...could you just be imagining that now that you suspect a problem? The brain is a funny thing. Run it however long or often you want and don't worry until it shows additional symptoms and enjoy the pool.
Al
Couple other things.
Was the motor casing discolored?
Make sure the vents are not plugged by critters trying to build a home. You should feel a good air flow.
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