Hi Bob, welcome to the forum!
It's really cool to see interest in using jet ski power and I always thought that the 12' Flying Saucer would be a great candidate for a classically styled conversion.
From the research I've gathered stemming from my own project build, the easiest method of doing a jet ski conversion is to cut the keel and transom sections (retaining the factory engine and pump mounting) from the donor ski hull and graft it into the Flying Saucer hull as a single unit. this at least eliminates a lot of issues regarding fabricating engine and pump mounting and powertrain alignment in the build.
Also, with this method being the most popular route for converting, there is more info here on the forum and out on the net regarding the issues that have been encountered and the various solutions that builders have used to take care of those issues.
You've got a good start already by having the donor ski in hand to gather all the measurements for the components, and with the typical jet ski having a pretty long powertrain I would definitely recommend stretching the FS the 10% to 13'. Keep the ski keel that extends below the FS keel narrow and long, and it doesn't have to project very far below the FS keel to be effective for loading the pump and boat handling. Also try to keep the ski transom portion that mounts the pump even with the FS transom, and behind the transom is even better. This reduces the turning response, or "twitchy" steering, along with better hull tracking.
This isn't the route that I chose to take on my project, but I've spent a lot of time researching my options so if you have any questions, I'd be happy to help!