The DI setup is a bit different than everything else Seadoo.
One critical part of the DI system is the fuel pressure. I am wondering if the fuel pump is getting hot and starting to fail. I would test the FP Pressure. At idle, with the FP and the air pump it should be 107 PSI. In your case, you should test it when it is cold and runs well as well as after it starts to act up.