Hey Mate,
If you haven't already done it the first thing you need to do is download a manual, you can download one from this site if you join as a premium member, or just google it and download one elsewhere.
It's not that difficult to remove the engine, probably even easier in a boat than a PWC. To free the drive-shaft you'll need to pull the pump. This is good practice, this way you'll know how it goes back together. After you remove the pump, remove the drive shaft, disconnect the wiring, hoses, loosen and remove the four bolts on the motor mounts and remove the engine.
You can remove the engine with a hoist, or a block and tackle, get two old spark plugs, break off the insulators and weld a large washer one each plug, you can use these as lift points. It's easier than you think.
You'll need to talk with your re-builder to see how much he wants you to remove from the block, ie: carbs, exhaust manifold, starter, flywheel, etc.
Lou