I like to over think things and complicate the hell out of them.
LOL! Welcome to my world Kyle.......
I don't think you'll have much to worry about with the 1200s performance in the Bullet. Fiberglass is a heavy building material for boat hulls. The Honda donor ski that I got for the TNT build had a dry weight of 798 lbs. with only 250 lbs. of it being engine and pump, so the hull with the hardware weighted almost 550 lbs by itself (it was freakin heavy to push around when I was cutting it up to dispose of it...). In comparison, the original TNT plans lists hull weight at 125 lbs. and with the mods I'm doing (stretching the hull 1.5 feet and turning it into a tunnel hull), the new bare hull is estimated at 200 lbs. and dry weight of the completed boat of about 600 lbs. (almost 200 lbs lighter).
Adding to that are the facts of the Bullet being a more efficient planing hull design than the ski, with less deadrise, or V, to the bottom, and being wider than the ski hull, you have a very real possibility of the Bullet actually being faster than the ski originally was (as an example, the Honda donor I got had a top speed around 65-66 mph. When I plugged the numbers for the Honda's engine and pump into my hull design program for the TNT, I ended up with almost 90 mph in the tunnel hull using the same horsepower.....

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As far as installing the Polaris power into the Bullet goes, there's several ways it can be done. The easiest way is to graft the center of the ski hull into the Bullet design, which allows you to use the original pump intake tunnel, pump mounting and engine mounts for powertrain alignment. I didn't go that route due to the hull design, and because I wanted to be able to install and remove the jet pump with intake as one piece (like the full-size jet pumps), so I found out that the older Yamaha GP and XL1200s actually use a cast aluminum pump intake duct inserted into the hulls instead of being part of the hull mold like most of the skis (still have to fab a billet aluminum mount flange and adapter to install the Honda pump to it, but that's part of the fun....). There are also companies out there offering cast aluminum pump intakes for the aluminum mini river jet boats that people are building, but those intakes are PRICEY!!
One thing I learned a long time ago, since I'm not a welder, is that a lot of the cost of getting stuff fabricated and welded is the fabrication part. Getting aluminum welded is a LOT cheaper if you do all the fab work yourself and all the welder has to do is welding the pieces together.....