I put some mp4 videos into a working iTunes U folder. How do I get iTunes to recognise them?
The meta data for a video file destined for iTunes must have the right internal identifier for the file type.  

For example, I might rip a DVD then encode it with handbrake.  If I throw this file in iTunes to move to my iDevice it thinks it is a home movie.  Slight inconvenience.  I use a free program, meta z, to set the internal identifier to "movie" and now it will show up in the right place.  Meta z also can set cover art and other web scraped data to make rips look professional.  A similar kind of processing needs to happen for iTunesU content.

Youtube will not preserve the internal file meta data that iTunes needs for the file to be identified as an iTunesU file.  Meta Z can set whatever bit of meta data needs to be set for the file to be associated as an iTunesU file.  iTunesU is in the video type dropdown in Meta Z so it should work though I have not personally tried it.  Though you will also have to set all the other meta data too, which may be annoying.  

Meta Z is free so give it a shot I guess.
Griff.github.io/metaz/