I like how you think and I have been in the same position as you, so from experience I want to tell you this.
Download a clean, untouched source. I would start with Ketchups, clean v15, 18, or 19 source.
With the latest Visual studio, since the newer, the better right.
From there start to edit small things, or big things doesn't matter.
Get some different sources, randomly, see what they have and include their "custom source" in the clean one.
There will be problems from time to time, as always there is with programming, but keep on going.
Keep backups and backups of your backups before editing anything, will be needed.
Sometimes you will be stuck and nothing will work, either find where the problem is or unpack one of your backups and start over
Find something in the game you like, make it better.
When you copy over different modifications, they are most likely buggy as hell, make them better.
Can't really tell you much for what to do, but like I said in the beginning, start with a clean source, either of Flyff V15 or newer V19. (21?).
When you have an idea of how the source is built, you can start to make your own modifications, addons and whatnot.
Don't be afraid to ask for help in this forum, even thought it seems like theres no one here, there are a lot of people just watching and hiding hueuhe