Axial flow pump....
No, you shouldn't have to change the single stage, axial flow pump since seadoo has used this model in serveral different applications.
As for changing out the motor, you'd also have to look at weight, motor mount and measured distance for the drive shaft. I'm not saying it can't be done and I don't have any hard core research to support that fact, only in conversation with others.
Like you said, lights and the bilge pump, etc....these are generic, but when you get into other components, the mpem has to identify these to allow the boats electrical circuit to be complete. I know when I was reading the manual for the 2005 4-TEC (which I'm sure your not wanting to use) engine, you have to have the mpem re-programmed to add any other accessory, like a bilge pump. Don't ask me why, I don't know that. It's just what I've read. In what your wanting to do, if you put in, lets say a 947, then where you may have 2 wires coming from your neutral safety switch, the other may have 3 wires.
If I were going to create more ponies for my boat, I'd probably trick out the 787. Although what I said about the engines life span is true, the 787 is one of the most reliable and simple motors to work with. I tear mine apart on a regular basis just to look for any potential problem or to keep it clean and the parts free. When I first got it, all the nuts and bolts were practically impossible to remove. I had to cut the carb studs on the pto side just to be able to rebuild it. Now, all my bolts and studs are torqued properly and removed yearly for inspection............sorry, going off on another tangent. To do what your wanting to do, you'll need to have some type of blue print for motor weight, hull design etc.....
There was a video thread in the forum last year where someone supposedly put a mazda engine in a boat. But all you ever saw was the engine. For me, there was no proof that the boat was actually powered by that motor. And another video here just recently of a pwc powered by a diesel engine.
You've got a good challenge on your hands. I'd be interested to see what you end up doing. Keep us up to date!........