Tim here - Thanks brokentone! Glad you like it.
We built a lot of it ourselves with some great tools. The player is video.js and we use popcorn.js to sync the transcripts, outline and player timecode. The video is transcribed and timecoded with Zencaptions and the transcoding is done via Zencoder. Let me know if you've got any other questions. Happy to help. Or better yet, shoot me an email: tim[at]heavybit.com.
Right now we're working out some kinks with V1, but we're hard at work for the next version. Suggestions welcome. :)
See, I immediately went to read it because the video was an overlay and I associate those with navigation tools, but was frustrated when the overlay turned out to be so large; I then deleted it without thinking about it and read the first paragraph before realizing it was a video.
So, I think you should shift it down the screen, below the bio, and keep the effect you currently have where it moves with me as I read the transcript.