The muffler was likely damaged because the weeds clogged the intake which is located inside the pump by the impeller. If the impeller can't produce enough pressure, there's no water coming in to cool the exhaust sytem which overheats and can literally melt plastic parts. Hopefully you understand that part now and are more careful with weeds. For some, jet boats are not for them if you happen to be in heavy sea weed area. If you do suck them up, you need to get them cleared if it's that bad. Most weeds are chewed up and spit out, but some of the heavier stuff won't. You're left with two options. One, go in the water and pull them out by hand. Two, do a "flat spin". Accelerate so that you make the biggest wake possible (note, speed isn't important). When you have a large wake behind you, spin the boat as hard as you can to one side. As the turn starts, kill the engine via the kill switch. That will spin the boat around and you'll start back surfing the wake. The water will then enter the jet nozzle from the stern and flush in the opposite direction and push weeds out the intake. But this only works sometimes and won't remove weeds stuck inside the impeller. Just on the intake grate. You can do it a few times in both directions.
The seal you're speaking of is likely the carbon seal. It's the seal that goes around the drive shaft as it exits the hull to reach the impeller. The seal is incredibly important. If it's damaged, it will cause a leak, potentially massive and can literally sink your boat. It's made of carbon and can wear out due to a few factors. Heat is usually the big culprit. This is why you are not suppose to flush the engine out of water for more than 2 min officially, and most do it well under 1 min at most. That seal is NOT cooled out of water even if you have a hose on it. Another reason is engine alignment, but that's pretty rare these days. If it's out of alignment, it will rub against the seal in one spot and wear it out. Another big/common reason is if you suck up something. I suspect this is what happened to you. If you suck up something hard, it can break that seal as well. Not as common but it does happen. Ropes especially. What type of seaweed do you have? Is it like sea stuff, super thick? That can behave like a rope.
So you likely need to replace your carbon seal. But it would be a good idea to confirm before going ahead and doing that. One of the common methods is while it's on the trailer, turn off the bilge pump and dump a bunch of water in the bilge so that it covers the drive shaft. And see if it comes out the bottom from inside the intake grate area (forward of it). You can also turn on the engine a few seconds once there's water in there to see if it accelerates the leak. Again, don't run it too long.
Carbon seal replacements are doable, but without experience and a special tool, they can be difficult. Check your PMs for more info.
