@ScarabMike might be able to help you. On our Yamahas, for those things that we can't get out through the Yamaha clean out ports, we often look into the intake closely with a bright flashlight and even use a mechanics folding mirror, and also into the nozzle end of the pump. We can almost see all of it but not quite. It is easier if we have to get at something stuck inside the pump, to just remove the pump assembly. But I haven't actually read about pump removal on the Scarab and don't know how easy that is. Rocks can be very hard on both the liner and the impeller. You may not have anything left inside but the damage may be causing the cavitation and noise. I will keep an eye on this thread, so if you would be so kind as to post up the process and your results, it will help others that follow along after.
I also wanted to welcome you to JETBOATERS.NET
@Amanda Herrick , while our roots have been mostly Yamaha, we have members from the other jet boat makes out there, and Scarabmike is the Forum Lead for the Scarab, he may be able to give you some first hand. The more member participation in that forum will just help in the long term for everyone. Welcome once again and looking forward to seeing you with it back in the water in good order!