Right now, only 2 is correct. However, 1 and 3 could be correct with a few minor modifications.
When I’m doing something enthusiastically, it is the only moment when I can feel alive.
This sentence sounds awkward because of two things. First, your usage of the word "it" is wrong. Here is the right way to use "it". Let's say I have a car, and I want to tell you that it is red and fast. So I say:
I have a car that is red. It is really fast.
In the first sentence, I don't say "I have a car that it is red" because I am directly referring to the car in the same sentence. The "it" is unnecessary.
I do say "it" in the second sentence. The second sentence really means "The car that I just mentioned to you is really fast." However, it is a lot easier to just say "it" and you understand this to mean my car from the context. Actually, the definition of "it" is
used to represent an inanimate thing understood, previously mentioned, about to be mentioned, or present in the immediate context
This sentence also sounds awkward because you use "when" twice. I would drop the second when and make your sentence "When I'm doing something enthusiastically is the only time that I can feel alive."
It is when I'm doing something enthusiastically that I can only feel alive.
This is correct, but it's not what you're trying to say. This means;
There is a time that the only thing I can feel is the feeling of being alive. This time is when I am doing something enthusiastically.
I assume you are trying to say:
If I am not doing something enthusiastically, I do not feel alive. If I am doing something enthusiastically, I do feel alive.
To fix this, move the only to before "when"
It is only when I'm doing something enthusiastically that I feel alive.