Can't beat the reliability of an OEM yamaha driveline though!
I have never owned a stock yamaha yet and never had an issue that wasn't caused by my own neglect or ignorance. My current ski's were built up from bare hulls and have been mostly trouble free for over 3 seasons. My wife's piped and ported 760 has been the most reliable ski I have ever owned. My Matrix has been as well except for a rubbed cable that was always draining my battery. The rest is routine maintenance from riding salt like a failed stator, midshaft and steering cable.Engines haven't skipped a beat since being built and tuned.
Not knowing the full story and not trying to be hard on you but the problem is most likely you or your current mechanic. Unless you have learned something new or switched mechanics, what's to say that the same mistakes won't be made during the swap and you won't end up in the exact same place? I know it sounds harsh but I my intent is not to bash you but rather to get you to just take a deep breath and look at this from another angle. Ask for help, do some more research and don't give up on what you currently have.
There is always some missing piece of the knowledge puzzle and a single ski in all our pasts that hands us our ass. Mine was a 98 GSXL that I struggled with for two years after a major engine upgrade. I owe all my current knowledge to that single build. It taught me more about 2 strokes than all the other ski's I have owned combined and I wouldn't take a second of it back. I wanted to give up at times but I suffered thru and kept learning and that experience has made me a better mechanic.
After all, if everything worked right the first time, what would we have learned?
Edit: I read back thru your threads and read about your engine troubles and I feel your pain. You have a real head scratcher where you should have a kickass and reliable ski. We had similar issues but were running way smaller domes to achieve the same compression numbers you are posting. We ran 32 cc domes and backed off to 34 cc domes to keep from eating pistons.