If you have a good transcript, you can temporarily upload the video to YouTube (mark it as private if you like, it only needs to be accessible to you) - then in the "Captions and Subtitles" options, upload the plain text transcript.
YouTube will sync the transcript to the audio, (removing the ambiguity of it having to guess what is being said, as you're telling it that - so now it knows what words it's listening out for) and you can download the resulting automatically timed file as an SBV or SRT type file.
It's not 100% perfect, and is something of a hack, but it usually works pretty well. :)