Fortunately most of the inferior US designed ignitions I made seemed to still work on the superior UK spec electronics. But will forever remain a mystery to me why someone would remove good UK spec electronics to replace it with my rubbish
Looking at the wiring, it LOOKS like you have 3 sensors mounted on the flywheel, each one that corresponds to firing one of the 3 coils. Is that correct? If so, you could replace your CDI with 3 programmable dirtbike CDIs, and not have to change/add any mechanical hardware. There will be a little challenge in getting all 3 to power off the single winding that was used for charging the CDI on the stock system. So it might be easier to use a 12V DC type dirtbike CDI, there are several bikes/quads that used those. Look for an electric start bike/quad programmable ignition. The downside of this is that you have 3 separate ignitions. Cost is higher, and you need to individually zero out and adjust/program them.
There are several ignitions available for Yamaha watercraft. Programmable, multicylinder, etc. Cost is a little high, but not too bad. The main issue, would be adapting them to work with your setup. There are a lot of unknowns when you try to adapt one aftermarket CDI to work on another setup.
4 stroke stuff might be able to be modified to make it work, you just want to really be sure you know what programmability range it has. Some may only allow a small range of adjustment, and you need a good bit more to get the most out of the 2 stroke.
The MegaJolt would be a good option, although it might be a bit challenging for someone not familiar with electronics. It will require more fabrication work for sure. But I'd guess it'd be easier to get help with the electronic side of things on the forums dedicated to the MegaJolt.