How to email an additional letter of rec?

For my Harvey Mudd application, I submitted two letters of rec for English and Music (max: 2) when I turned it in. However, I didn’t know that the rec letters were supposed to be from a math/science teacher and a humanities teacher, so my application is incomplete because I didn’t submit a rec letter for math/science. My computer science teacher has already written a letter of rec for me earlier, and I have to submit his letter by email to Harvey Mudd.

Should I ask him for the rec letter (which confuses me because of the FERPA waiver stating that I can’t view my rec letters) and send it myself, or should I just ask him to send it? If he sends it, then would it be fine on my application that I would technically have three letters of rec now (Comp sci, English, and Music)?

You should contact the school and ask them how to submit the additional letter of recommendation.
As for it being okay for you to have three letters; yes it’s fine as long as you have the needed two any other letter is considered extra and if anything, may help your application.