Yes those bearings are pretty noisy! The crank does press together but must be trued during assembly so it's in phase. It's probably not worth trying to attempt it yourself, needing special tools, V blocks, dial indicators, rebuilt cranks are pretty cheap, SBT has them, you could send yours out to Crank Works for a rebuild or buy a new Hot Rods crank. On used cranks be careful, I bought a used stroker cylinder and matching stocker crank on Ebay from an actual jet ski performance shop in So Calif, both were advertised good, inspected, only 8 hours of use and ready to go with new Wiesco pistons and rings, fresh hone. WRONG! Piston to cylinder wall clearance was at .007 and the crank was twisted out of phase by like an inch or more and the bearings were noisy, so both needed rebuilding. I have pic of the crank I'll try to post.
I see you have a dry pipe, I had that pipe on my old ski as we'll, make sure you have enough octane if you run wide open at times, I made the mistake of running 87 octane @ wide open throttle and it took the top of my piston off. After that I ran 110, I like to be able to hold the throttle open, then later blended 50/50 110 with 91, no problems. Then Gave my wife the ski so after a while seeing she never ran it wide open I used 91 with no problems. Now my friend owns it so we are back to blending, now it's 1 gallon 110 with 4 gallons 91 so it's close to 94.7 ish. He Rec rides, jumps wakes most, occasionally holds it open a very little. Friends that want to ride it always seem to pin it open even when you tell them not to so watch out. Got electronic water injection? Helps the low end