Im in the process of putting a yamaha motor in my js550. Its not cut and dry. Im using my stock js550 pump and driveshaft for now. It will be alot like a fx1, you will have cavitiation with a small pump. Heres the issues with the swap.
1. couplers and motor hitting battery box
2. motor bedplate
3. ebox mounting
4. Exhaust
Foximus covers alot of this in his 550 build. This is not near as easy as the kawi motor conversion. Im having to get a js550 coupler tapped out to fit the yamaha motor because the tigershark and yamaha coupler combo wont reach due to the battery box and the tigershark coupler not having a long enough neck. But yours might work cause your using the 550sx driveline, the js550 driveline uses couplers that have the longer neck where your coupler on the driveshaft is flat on the back. I will most likely have to shim my driveshaft coupler a few washers to reach as well. Keep in mind that foximus grafted his pump section in and was able to set his up however he wanted to.
Blowsion sells kawi couplers for yamahas, but I dont wanna spend $100 for just needing one coupler.