The schedule is fine with me. vs The schedule is perfect for me. vs The schedule sounds great to me.
I will have a 2-month rotation in a clinic. My doctor sent me an email including detailed schedule or arrangement of my rotation. I totally agree with the schedule. Meanwhile, I want him to know that I am really grateful. How should I respond to his email?

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I would keep it very short and simple, but professional. Something like, "Thank you for the email. The schedule is fine.  Regards, XYZ"

The "with me " in "fine with me" is redundant. So, I'd leave it out. Not necessary. The "perfect for me" and "sounds great to me" sounds like you're writing to a friend who invited you out for a pizza. It's too informal. Way too friendly.

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Either of your second two options will sound more grateful and enthusiastic about the schedule.   The first option (fine) sounds as though the schedule is acceptable, but not great.