For the video, you'd probably want to do a stream copy, which will retain the original quality and save you from having to potentially wait a long time for it to encode:
I've seen you mention those tools a couple times. I'm familiar with ffmpeg. Does convert also cover the MS Office file formats, as this tool purports to?
The convert tool is part of imagemagick and only works on image formats as far as I know. I personally use pandoc to do similar conversions on documents and ssconvert for spreadsheets.