A faster motor doesn't mean a faster car. I know it sounds odd but trust me on that. The stock motor in the Rail is 36mm in diameter wheres the CC 2200 motor is 40mm. Bigger diameter cans make more torque and the Castles 2200 makes gobs of it. So all you have to do is gear it up more to get the same or higher speeds than with the less powerful motor. Also another thing to keep in mind is motor efficiency. Wheres the Rails motor does OK in terms of performance it gets bloody hot quickly too. It isn't very efficient and lot of power it consumes ends up as heat instead of power that propels the car forward. Castles motor is a much better motor, with better design, bigger, more powerful, better components used inside,.......well you get the picture.
Diffs are pretty good in the Rail. Proper 1/8th diffs and they have been doing just fine for me (and I am very throttle trigger happy). What I recommend is you disassemble them, clean out the grease in the front and rear and fill them with silicone diff fluid. I used 30K up front and 15K in the rear. Works for me. After that make sure you fill the diff housings with plenty of good grease so the pinion and the ring gear have plenty of lube.
Center diff has silicone fluid in it (very little from factory) but since you are going to have to change the spur gear clean out the diff case and fill it with silicone diff fluid as well. I used 500K in my center diff which is ridiculously thick but I love wheelies. Something about the 30K range would be adequate but I hate unloading too much power to the front wheels. The thicker the center diff fluid the more power will get sent to the rear wheels. All depends on your driving style. Don't forget the 48T spur gear while you are there. Part number MV22832.
Don't worry about the center dog bones. They are plenty strong. Also the front CVDs and the rear dog bones have stood up to the test of the bigger motor just fine. Actually it is pretty strong buggy and should do just fine. Keep the diffs standard and just do to them what I told you.
ESC, like I said you can leave it for a while but if you want you can get it upgraded too. Seems to do a lot better with the better and more efficient motor. Stays pretty cool. With the 17/48 gearing you should be pushing over 50mph on 4S with ease. I drive my Rail (well it's called a Cage here) through grass, dirt, pavement and everything stays nice and cool with that gearing.
Hope that clears up a few things for you.