Q: Moving iTunes from old Mac Mini to newest Mac Mini

Splitting the iTunes collection (media vs. controlling files) makes it really messy for trying to transfer them and get them back together.  What might be easiest would be to just transfer the files on the old internal to the new internal, more or less as you have them set up now.  Then plug the external into the new computer and start up iTunes more or less the way you would on the old computer.  Now go to iTunes Preferences. Make sure the preference settings are for iTunes to put media on the internal drive's iTunes folder.  I haven't done this myself but I believe at this stage iTunes will ask if you want it to copy files and folders to the designated Media location and also if you want it to organize items (make sure those preferences are set).  Basically this is consolidating the collection on the new internal.

Here's some background:

What are the iTunes library files? - http://support.apple.com/kb/HT1660

More on iTunes library files and what they do - http://en.wikipedia.org/wiki/ITunes#Media_management

iTunes 9: Understanding iTunes Media Organization - http://support.apple.com/kb/ht3847

How things should look when you're done:

Image of iTunes folder structure Dec. 2011 - https://discussions.apple.com/message/16923545

see also:

Image of folder structure and explanation of different iTunes versions (turingtest2 post) - https://discussions.apple.com/message/13025536

What are all those iTunes files? - http://www.macworld.com/article/139974/2009/04/itunes_files.html