I never followed up on my waverunner engine swap. I couldn't find anyone willing to take on the swap so rolled up my sleeves and did it myself, I don't think anyone wanted the risk of it not working correctly and had plenty of other work to do. In the end it was probably a good thing given the amount of money I probably saved, especially now that I likely need to do it again. Hardest parts ended up being figuring out how to rig up something 11' high to lift the engine out with and getting the stupid water hoses detached from the waverunner engine as the tabs on the clamps were rusted off. The hatch openers were kind of a pain to get back on without help also but the fact I call this out shows how few real challenges I ran into, it really is a very straightforward swap but takes some time.
Before doing anything I decided/determined that I needed to keep the boats wiring harness and ECU with the boat which caused me to disconnect things a bit differently than I have seen in other writeups on this site. Note that keeping the ECU with the boat means that it still reflects the hours and stats for the original engine but I know how many hours were on both engines a the time of the swap so I will always know how many hours the replacement engine has. The waverunner does not have no wake mode but had a beginner mode and security key fob, not sure how much of that is tied into the ECU but wasn't going to risk being stuck with that just to have the correct hours.
I did find this writeup on greenhulk for removing the waverunner engine without removing the ECU or wiring harness which I basically followed on both the waverunner and the boat -
Yamaha VX110 Engine Removal post #3. Using this method there is no need to disconnect fuel lines on the boat which seems to have been a bit of a hassle for some in other writeups I have seen. This is because along with the ECU and wiring harness the entire intake with the throttle body and fuel rail stay with the boat. I wasted a lot of time labelling everything as I disconnected things but I believe all the plugs are unique and everything laid right back in place such that it was obvious where everything should plug in so I never had to look at any of my labels (and I am the type that always reads and follows instructions). Below are a few pictures from the swap, after hooking everything back up it started up an ran like it had always been there first try.
Here is the engine ready to be lifted out of the waverunner. Note the ECU, wiring harness and intake/fuel rail removed from the engine and laying in the footwell. I also pulled the airbox so the engine could be shifted forward when removing.
This is the engine with cracked block ready to be lifted out. Again, notice the ECU, wiring harness and intake/fuel rail removed from the engine and just set aside on top of the port engine without disconnecting the fuel lines or any wiring that didn't need to be. I put tape over the openings for the intake but probably should have just stuffed old socks/rags in them because I ended up having to remove some tape residue when I pulled it off. The big round air filter box was unbolted from the wall of the boat and removed to make room. I was able to just wiggle free and set aside the section of the exhaust that you see removed after loosening the clamps on the rubber connectors and it went back in with similar coaxing.
And here it is hoisted out and enjoying the view. The top of the ladder was strapped tightly to a tree which gave the whole hoist rigging much of its stability. Note that rather than removing the engine hatch I just disconnected the openers and made sure it was supported (with a sturdy trash can on top of an old tire) - after lifting the engine I had to carefully back the boat up and close the hatch before I could pull the boat out from under the engine. I was able to carefully hoist it out without any help, it is light enough that with care you can maneuver it around a fair amount with one hand while working the hoist with the other. I was glad I had someone help me drop the replacement engine in though, come-alongs ratchet in better than out and for some reason dropping the engine in seemed harder. The engine in the boat had no shims but the waverunner did have some, I didn't end up using any shims - it did take some yanking on the engine to get the coupling lined up and spaced properly.
Hope this helps someone else. While I'm fairly handy with mechanical things I wouldn't even call myself a weekend mechanic and would say this mostly just required some time and effort, nothing terribly complicated about it. Just be careful the engine doesn't bump any fiberglass on its way in or out.