Quite possibly when the basket area heated up and warped you could have opened an air leak at either the basket lid or the pipe fitting. Don't understand why the difference in behavior between the main and skimmer ports. Almost sounds like the leak could be at the valve but I assume that part didn't get hot....unless it is hooked directly to the pump. You can try using a squirt bottle to squirt water around the suspected areas and see if it gets sucked in when the pump is running and the skimmer line selected. Can also use a piece of small diameter hose as a stethescope however the pump noise may make it difficult or impossible to hear the air leak. It also sounds like you had a leak somewhere in the system all along because of your need to close the suction valves to prevent water from draining back.
Hope this helps.
Al
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