My solution was this: set up a separate laptop/computer to transcribe on,that way you can pause the footage rather than having to switch apps all the time, it also meant you could type at your own pace. Even better if you have someone sitting next to you who could control FCP.
I also applied a timecode generator from the effects bin onto the selected clips, seeing large type TC at a glance made life a lot easier.
John doggett-williams