I work with legal transcripts in PDF format. I will then do the mark-ups using red ink and highlights, and when finished with the transcript, I'll email only the annotated pages back to you.
I find misspelled words, homonyms, and transposed words. I check for proper spellings of names and places; I research medical terminology and verify dates and addresses. You'll then be able to make any changes to the transcript as you wish before you turn it in. You can also choose not to use the annotations I suggested, as all my corrections can be looked at as suggestions.
If the transcript is very long, I would prefer that you send them to me in a series of a manageable amount of pages, as in 50-100 pages at a time. That way as you are working on the latter part of the transcript, I will be proofing the first parts, and I'll send them back to you as you send the latter part. In that way, I can return them to you as I finish them.
I'll send each new client a preference sheet that you fill out and return to me. This will enable me to proofread the transcript per your personal preferences. My goal is to have the transcript as close to perfect as we can get it.
My go-to resources are "The Gregg Reference Manual, Court Reporting", and "Bad Grammar/Good Punctuation, and the Merriam-Webster Dictionary. But my favorite resource of all is my fellow proofreaders. I belong to a group where I can ask any question regarding punctuation and grammar; they are very quick and so very helpful to answer questions for me.
I will never, under any circumstances, break any confidentialities that may be in place in regards to transcripts that may come to me, should they be of a sensitive nature.