Taking on water

[71Stngray]

I have a 2004 SeaDoo RX/DI and this year when I put it in the water and have it anchored it is slowly taking on water. After 5 or 6 hours the hull is filled up almost to the top of the engine.
I put it on the trailer and I do not see the water leaking out anywhere other than a very slow drip through the bottom of the hull where the gel coat is damaged from a scrape. It doesn’t seem like it would fill that fast from that spot on its own.
Also wondering as there are two garden hose threaded openings on the back. I believe one is an engine flush port and the other is an exhaust flush port. Is this correct? Are they both uncapped when in use?
Could it be coming into the exhaust flush port and leaking into the hull somewhere?

 

[murphn8r]

i would put it in the water take the seat off and start looking to see where. it should be noticeable if its filling fast

 

[71Stngray]

I filled it with water on the trailer as it had already been filled in the lake, and no leaks, however after I drained it and got it running again I noticed something flapping on the back and water coming out of it. It appears to be a diaphragm that has come partially out. It connects to a 2” hose on the inside then to the waterbox on the exhaust. I assume this diaphragm may be the issue?