I don't think the large hull will affect you too much. Remember that these engines are also used in 23 ft wake boarding jet boats. Granted, there are 2 engines in those boats, but consider how much heavier that fiberglass hull is than your aluminum hull. My setup weighs about 1200 lbs, with a 48 in beam, and about 12 ft in the waterline.
If you still have the factory controls, it will be plug and play, unless you want to extend your harness, then just make sure to splice the wires one at a time when you're adding in the extra run, so you can keep track of which is which.
My engine, harness, and ECM came out of a boat, and I did not have any factory controls. I had to do a lot of figuring and modifying to fit my existing harness. In fact, I'm using the tachometer from an AR-230 jet boat. It uses an 8-pin plug, which I was unable to find, but was able to make my own pin connectors and then sealed it with marine grade silicone. Works just as good as a plug.
As for the reverse bucket, it should do OK. I'm using an XL1200 pump in my boat, which has a very small reverse bucket, compared to the newer Yamaha 4 strokes. Still, it's ample enough for my application. If you're going to use a reverse bucket off a Yamaha FXHO, that should be more than enough. I say that because we own a VX110 Yamaha, and if I let off the throttle at 20 MPH, hit the reverse bucket, and then hit the throttle, the bow of the jet ski will do an instant nose-dive, and it will almost put me over the handlebars. It's the same reverse setup on the FXHO as the VX110 and FX140.
