There is no real difference, maybe the latter is more friendly.
I’d use the first one if I really wanted to know how I was found, and the second one to show I’m surprised to be found.

I don’t think there is much of a difference. Both are oral forms of asking a question, and I’d say the first one is less graceful.

In english, you can compare: How did you do to find me? versus How did you find me?. Using the faire word is unnecessary here. Maybe it is used more often but if you have the choice chose the second option.

A more formal way to ask this question would be to change verb and subject: Comment m’as-tu trouvé ?

Well grammatically the second one is incorrect. The second sentence is not chocking when you informally speak but it may be considered by some people as incorrect even rude.

Heard in spoken French in everyday speech: Comment tu as fait pour me trouver?:

Better grammar, if you care about that: Comment as-tu fait pour me trouver?
People actually use the first one, all the time, in everyday speech.
Translation: What did you do to find me?

Heard in spoken French in everyday speech: Comment tu m’as trouvé?
Also expressed as: Comment m’as-tu trouvé?
Translation: How did you find me?

Conclusion: the two sentences are not the same thing and they have more formal and less formal ways of being said.

There could IMHO be a difference between the two sentences, depending on the context.

The second sentence’s (“Comment tu m’as trouvé ?”) meaning would be “How did you find (my performance, my speech…)?”, whereas the first one means “How did you manage to find me?”. But this is hard to decide without the context.

Now, in spoken language, the second sentence could be understood to mean the same as the first one, but it could be ambiguous.