Hi Sean,
You should have better started by converting the MP4 to a more editable codec. Beside not being supported by FC, one of the problems of editing MP4 is that being LGOPs, you have no frame accuracy.
If you have the sequence ready, change the sequence to 8b Uncompressed or Prores and export.
After you will need to convert that to MP4/H264 to upload to YouTube.
rafael
http://www.nagavideo.com