Well, while what you want to do is very possible, if you're a complete noob in coding CNS, then you're going to have a tough time with it. Also, know that transformations, unless done correctly, the hard way, are going to break your character from being juggled and grabbed by other characters. There are other complications with it as well.
In terms of the number of CNS files, the reason you see such a varying amount is because it's about organization. For example, I like to split major parts of moves into separate CNS files. If I know my character will have a lot of thrown weapons, I might put all of the helpers of those moves or even the moves themselves into a separate file called thrown_weapons.cns. Again, it's up to you. There's no rule. You could have 1 or 10 if you want.
Now, since you're so new to this, I would start here: http://elecbyte.com/mugendocs/mugen.html. Read it 100 times if you have to. There's everything you need to know right in these docs. Bookmark them and reference them often. Before looking at the lists Triggers and State Controllers, I would suggest reading the CNS guide there. It teaches you about the various aspects of state coding and other portions that people might not realize are required to code in the procedural *wrapper of CNS.
