I now want to take these upgraded files and load them onto a dedicated Aurender music server that runs its own software for playback. When I made all of the changes to my music, is it done at the library level and the original music files are untouched, or things like artwork and genre changes I made re-embeded into the original files?
By default, MC should be writing all of the tag changes back to the files. Not all file types support all tags, but most of them should be there including the major ones like Artist, Album, Genre, etc. Double check your MC setting for this to be sure:
Tools > Options > General > Importing & Tagging > Update tags when file info changes > (checked)
What is the best way to get my newly cleaned up collection loaded onto my new toy?
Good question. Jim's recommendation is a good one. The Rename, Move, and Copy tool can copy all of your files (or a selection) to another location and use rules for what directories to put them in. Things like Artist/Album/SongName for example.
However, the RM&C tool has a limitation of NOT showing status while it does it's copies. You'll see a small indicator in the footer that says "X remaining" or something like that, but nothing that tells you detailed status. For this reason, on big copies like this, I prefer to do one of two things:
A. Use a dedicated file copying tool to do the copy. I like rsync because it's very sophisticated, is included with OSX, does incremental copies, and it runs from the command line. I like command line because I'm very familiar with it. If you're not, you should look somewhere else, as rsync isn't a very friendly tool for first time command line users.
B. MC includes a HandHeld sync tool. This is designed to copy music (and/or video) files to a portable player. It can be set up to point to a path on your disk. This could be the external disk used by your Aurender. You can tell it what files to sync, via playlist, or just make a single smartlist that contains everything. Handheld sync shows detailed status as it runs, and seems to work as you'd expect. If you have complex directory structures they may be lost in this copying process though: The originals will be untouched, but you won't get the same directory structure on the destination disk.
http://wiki.jriver.com/index.php/SyncNo matter what you choose to do, I would start by playing with a few files, or maybe a couple of albums. Get the techniques down and then apply it to a larger set.
Good luck!
Brian.