Hooked the red wire for the voltage regulator back up and checked the compression. Compression seems good, very similar to what I had before. About 155 front cylinder, 145 rear cylinder. When I pulled the plug they didn't smell rich like gas, in fact had almost no smell. Makes me think it is fuel related.
I also checked the muffler, I was able to tighten up the front two hose clamps, but I don't think they were leaking. In fact since the ski was running well Saturday for about 30 minutes I don't think that was the issue. I'm leaning toward the fuel supply. I did notice quite a few air pockets in the fuel lines.
Will take it back to the dealer on Wednesday since I do have a few days left on the warranty. If they work on it I believe they give you another 30 days warranty for that repair. If I didn't have the warranty I'd probably start checking out the fuel selector and carbs, but will save that learning experience for another day.