Thanks for your advice everyone. It has 4 new coils, plugs and wires, and CDI box just replaced. I'm not getting a power pulse to one cylinder most of the time, especially at low rpm. There's a second cylinder (same bank) that is intermittent as well, but gets power more often. When trying to get the boat on plane, it starts off with 2 cylinders and bogs horribly. Then as the boat starts to slightly plane and pick up a little speed (5 mph tops) the load lessens on the engine and like an on off switch you feel another cylinder kicking on/off. After about ten seconds of that I get the 4th cylinder doing the same thing. It's like a shot of nitrous each time, and suddenly the boat launches like a cannon and runs perfectly until shut down. At full speed it runs 5,800 rpm @ 56 mph (with GPS), so I'm assuming the prop is fine.
I did use a spark tester, and see that the two cylinders on the right side will not spark during cranking. Then after it starts the bottom right cylinder starts firing, but not when it's under a load in the water. The top right cylinder really takes a long time to wake up and fire. The compressions are all in the 120's and I just rebuilt all the carbs.
I'm obviously not too familiar with this engine design but the last two stroke I had with this problem on was a Polaris 1050. Those engines had a well known problem with the stator and there was even a recall on them because it would internally short and take out one individual cylinder. In that case it was easy to troubleshoot with an ohmmeter, but it sucked because I had to pull the engine to change the stator. I've also read on a CDI troubleshooting write up that in rare cases you can have a weak magnet on the flywheel that could take out just one cylinder, but at high rpm's the magnet will be strong enough since this type of ignition gets stronger as the RPM's increase.....not sure how accurate that write up was.
Anyways, I was for some reason thinking the timer base and stator were an assembly together- but I guess not.