There is a lot of information in the X2 section. You should spend some time there.
If you stick with the 650 motor, then there are a lot of 650 pipes that are compatible with the hull. Keep it simple. Stick with what has been designed to fit.
It is best to go with a waterbox made for the X2. With that said, the 650s ingest a lot of water through the exhaust. I think it is at worth at least a consideration of a left in right out waterbox with a high point after. The superjet water box will fit in the nose and a B1 exhaust outlet will fit on the right side. You should have space to route the exhaust over the tank.
I believe a straight blade 15 pitch prop is a good fit for the 650 motor but I can not say for sure. I believe I had a 15 pitch in my 650sx when it was mostly stock but I'm not fully confident in that. I have a 750 big pin with lots of parts with a hooker 10/16 and that is too tall. I think a lot of 750 x2 run the 9/15, but I believe you may have troubles with any swirl style prop and the 650. Look through the 650 section for some more information.
If you decide to go with the 750 motor, it's still advisable to go with the 650 pipe. The 750 pipes do not fit in the hull. Don't beat on one with a hammer. The largest pipe I have found to fit reliably in the 650 hull is a westcoast 650 exhaust manifold, superjet B-pipe head pipe and a superjet b-pipe mod chamber. The westcoast manifold is a thicker casting and can be ported some at the head pipe. If going that route, a larger waterbox and outlet is advisable, the superjet box with B1 outlet is my suggestion, but I would advise against the bigger is better approach all together. A 650 motor or a 750 small pin with a 650 pipe avoids a lot of hassles and gives good results with the right tuning.
The single 44mm mikuni carb pairs well with both the 650 and the 750 motor. The superjet 44mm airbox works very well when rotated 90* to face forward so it doesn't hit the motor. I have dual SBN 44 on mine and was able to modify a XL760 airbox to fit.
