If I read the question right....you goofed. The only way to bypass the skimmer and pump baskets is to remove them. Is that what you did? Those baskets are there for a reason. That being to keep junk, including damaging junk, from the pump impeller. First guess is the leaves plugged up the impeller. If they get past that then the multiport could be plugged too because of the sharp corners and the way the water is directed internally. Possibly you could have plugged up the skimmer line too.
If this is what you did you need to kill pump power so your sure it cannot come on, then reach in through the basket and see if the impeller has junk. The multiport would most likely have to be taken apart to clean it out. Relatively easy. If the skimmer line is plugged then maybe using a garden hose into the entrance pipe in the pump basket can reverse flush it. Keep us posted and good luck.
Al
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