My first and foremost advice is to take any advice with caution. I spent a lot of years modding my X2 chasing a level of performance I never reached. Here are some things I learned...
No one with an X2 can tell you what to do. There is too much frakensteining going on. My Superjet was easily setup by a builder, and the same builder left a lot on the table for a friends X2. Many people with Superjets and other models have a performance formula. Since bigger pipes don't fit, and we put bigger motors that are restricted, tuning is always a problem. It's often best to stick with a known 650 setup and enjoy, but if you do swap motors and pipes, know that no one can give you set answers on performance.
Next is what is performance, and that is in interesting topic. I spent years chasing performance. I found out later that the people who claimed performance often didnt have it. I was never pleased with my X2, but people who said they had great running X2, said mine was better, or I rode great running X2 and politely disagreed. Surf X2s were often setup as 10 second skis, that is they were tuned hard for bottom, which in my opinion, was often not a well tuned ski but a ski that was tuned to perform half the time. I could get great, say, midrange, but I never got a well tuned machine. Maybe the kawi motor was just ported that way, but my SXR, setup by the same builder as my superjet, was excellent. I think the mix and match of motors, carbs, waterboxes, pipes, props, etc, makes a very difficult formula to solve that is rarely reproducable (due to availablity of parts and cost).
Hull mods, well, I never rode 2 X2 that rode the same. One I could ride, the other I couldn't. We mix and match so many steering, steering adjustments, nozzles, trims, ride plates, etc, it's just simply not like jumping from 1 Superjet/SXR to the next. It's hard to say on hull mods because the X2 just doesn't seem consistent in handling from build to build.
With that said, here's some things i found over the years of trying different things with my X2.
The X2 rides amazing with 2 riders. This lets me know that the pump cavitation and poor handling has a lot to do with weight distribution. It also explains why leg dragging works.
The X2 needs to lean with a lot of weight pushing into the pump to stay hooked up. Sponsons and nose fills can hinder that, and I'm not sure, dispite many years of advocating for sponsons and noses, that they are a great solution, although, they do have their uses depending on what you setup.
Ride plates tend to follow the factory down slope, which is for a ski designed for 2 riders. I am not sure why aftermarket plates follow this same design. The ski is nose heavy, and works best (in my opinion) with a heavy load on the seat, so why do we need ride plates that push the nose down? Why do so few Superjets and other skis with more rear set motors and poles for leverage on the nose not have rake to push the nose down, but the X2 with a more forward motor and no leverage on the nose has so much pressure on the ride plate?
Swapping the stock seat latch with a GP1200 latch is a great mod, and I 100% recommend that.
The best my ski ever ran was with a stock superjet waterbox and a 2" rear exhaust. For a long time, I thought the water ingestion problems we have came from the intake, but after blowing up a 650sx and having loads of water ingestion problems with my X2, I think the waterbox is to blame. A left in, right out design is probably best. I have limited time messing with this, but I think a superjet box with a B1 outlet infront of the carbs could be a consistent winner, and while disclosing a lack of evidence, I think it's the way to go.
The best running X2 I have been on belongs to a friend, running a small pin 750, 650 (westcoast?) pipe, stock waterbox, 44mm carb, striaght blade prop and UMI steering. It is not the most powerful ski, but it is the most ridable ski. I think that the limitations of the hull and waterboxes limit the amount of power we can get out of our skis before we start having a lot of tuning problems. He went with an X2 because of mine, and I strongly advised him to keep it as close to 650 motor specs as possible (has a 750 but stuck with all parts that would be on a 650) and that has turned out, in my opinion, the best advice for any X2 owner looking to enjoy an X2. The exception is that water is still a problem in the surf, so i stand by my opinion that the superjet waterbox, a high point over the tank and a right side outlet is the way to go.