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You very likely have something, perhaps a twig, piece of algae or plastic stuck in the jet. This is a common experience early in the year on the lake I live on.
Why is it difficult to remove the clean out plugs? If they are swollen you can rebuild them easily and cheaply with this part Rebuilding Yamaha Jet Boat Clean Out Plugs. It costs about $35 a plug and I believe requires removing and installing 8 screws. It is an easy job. After rebuilding Yamaha suggests removing the plugs after every outing.
I had never experienced new plugs so I had no idea how bad mine were.
I ordered two part # FOR-67609-09-00 - MANHOLE COVER REPAIR SET kits.
It took less then ten minutes to install the new lower parts. After doing so I found that my plugs would simply drop into place then press down to lock. There was almost no force required to pull them after unlocking. My five year old could install and pull the plugs.
Before the rebuild I had to lean on the plugs to seat them and pull hard to pull them. One had stuck in place at the end of last year. I had parked the boat under my deck so I used a small ratchet strap from the bottom of the deck to the plug and it came out easily.