Lauren,
It should be possible to change these to the correct form using CHSTRING. Please read about CHSTRING in the CLAN manual. Be careful with the letters "a" and "i". Probably best to do that one by hand unless you can make sure that you are not changing the pronoun "I" to i@l, and for "a" you definitely have to do it by hand. Note that MOR will be thinking that "a" is a pronoun instead of a letter unless you locate all the cases that have to be a@l.
Do this first with a test file to make sure it is doing what you want. Once you know your changes.cut file is right, you can apply it to all your transcripts in a single pass.