Hi, It would depend on what type of audience you were writing for. All of your choices seem "informal" and would be used in conversational English. All of your choices, in essence, mean that you "understand". For instance: 1. I see what you mean. 2. Do you understand the question? Yes, I got it. 3. First, turn right at the stop sign, and then go straight for six blocks. I got you. thanks for the directions. In all the examples, the meaning is the same. The meaning is "you understand".

1, 2, and 3 mean the same thing in increasingly informal style.

Sorry, they seem pretty much interchangeable to me. Can you give an example that sounds wrong? Maybe we could work from there. .... You can use "I see" for a wider range, maybe.