Stan did time before when he was younger
Stan had a very dysfunctional childhood growing up (he mentions half-sarcastically to Bill at one point that his parents argue all the time), and often got into trouble as a result, because he was a problem child. It finally got so bad that he ended up committing a very serious offense that landed him in jail at a young age. This was his wakeup call: the experience of being in jail not only scared him straight, but scared him shitless as well; he witnessed all of the things that go on in jail, including those that he keeps mentioning to Bill about prison rapes and sex slavery. When he and Bill are arrested and sent to jail, the memories of his previous time in jail are all that he can think about, and therefore he's terrified of reliving those experiences all over again.- He and Bill are just starting college in the fall, meaning that up until very, very recently, Stan was a minor, and absolutely would not have been sent to prison unless he committed some heinous crime like murder. No, Stan's behavior is not that of someone who's experienced it, it's the behavior of someone who's seen too many movies and is jumping hysterically to conclusions. One might as well posit that he spent his youth watching Southerners marry their sisters, because he talks about that in the exact same tone.
Judge Haller realizes the "Jerry Callo" fax is bullshit.
Judge Haller isn't stupid. He saw how unprepared Vinny was at the beginning, and how little Vinny knew about standard courtroom procedure. Is he really going to accept Vinny as an established trial attorney just based on the fax he was sent? I like to think the judge saw through the ruse and realized Vinny was exactly the novice he appeared to be, but decided to let it go after seeing how impressively Vinny ended up performing. His calling him "one hell of a trial lawyer" was meant as encouragement for someone he thought had a lot of potential but little experience.