I have just gone through Hell the past 4 days.
After all the excitement of receiving my first Mac, a rMBP, a week ago I set about the task of transferring my iTunes from Windows Vista to Mountain Lion. Back came the unpleasant memories of when I ran out of disk space on my old laptop and decided to transfer my iTunes Media Folder to NAS. Despite extensive planning and research I ended up loosing all my digital music and several photo libraries.
This wasn't going to happen this time.
I spent two days internet trolling to equip myself with the needed knowledge and awareness of the pitfalls to avoid. I am no dummy, having spent more than 40 years it the IT industry many as a PC systems consultant and build several computer systems for myself.
As the iTunes Media Folder was to remain on the NAS half the battle was over. So I thought. Consolidate and organise. Just change the default location of the MAC iTunes Media Folder via iTunes Preferences and replace the iTunes Library with the one from my PC.
Reloaded iTunes but shock no Music or Apps displayed in my library.

Everything was still on the NAS but iTunes had not picked it up. I remember reading about pathnames in the iTunes index being different on OS so I just added the Media library to iTunes again via the File option. Two hours later all my Music was back in iTunes albeit without some of the artwork. Only 10% of my Apps were present.
At this point I decided to restructure my media layout. Fool me. The NAS has a structure of Public share and within that three further shares: Shared Music, Shared Pictures and Shared Videos. iTunes expects everything to be within the Music folder under iTunes.
My iTunes Media Library had pointed at NAS>Public>Shared Music. I decided to change it to NAS>Public with the idea of moving the videos into the Shared Videos and the Pictures in to the Shared Pictures. Two hours later, my music reappeared in iTunes. Great I thought. Now to separate my pictures and videos. My media files were all over the place, some in music and some in Shared Music. Many had two references with duplicate Artist and Album folders and .APPLE DOUBLE filenames! Drats.
Times to abandon the reorganisation idea and go back to the original setup.
Changed the pointer to iTunes Media folder back to NAS>Public>Shared Music and then Consolidate and Organise. Oh dear. Files and references all over the place again. Two more hours of carefully deleting files.

Organise and consolidate. Why is it taking so long? What is it copying to were?

Check Media File locations. Yes, still on the NAS in the right location. Check using Mac Finder. WHAT!!!

All my media is now also on my new rMBP SSD and nearly filled it. Checked iTunes preferences and it has reset itself to my default Music library on my Mac. Grrrrrrrrrrr!
Delete media files from Mac, change reference back, consolidate, organise, pray.
YES. Finally everything in its right place and with the correct pointers, except for the missing 200 Apps.
Connect iPod Touch to iTunes and Transferred Purchases from iPod to iTunes. Apps restored to iTunes although the total numbers are different on iPod to iTunes.
Time to sync.
"Device synced to more than one iTunes, do you want to sync with this iTunes?"
Fair enough. OK. One hour later 1906 photos missing and Apps on iPod rearranged in random order and no longer in folders. "I Just Don't Believe It."

Next two hours spent rearranging Apps via the iTunes interface. By the way iTunes decided to automatically change the Photo Library to iPhoto from my previous setting. Why not? It has very much chosen to act as it likes despite my careful attentions. a further two hours, I am beginning to loose track of time now, and photos finally back again.
This is were I am currently. Artwork still to sort out, inconsistent counts for Apps, (iTunes also telling me there are 6 updates waiting to download but it also tells me there are none to update when I enter the store), Books and Podcast to sync.
I still have to ensure that the iPod does not automatically WiFi sync with the old PC iTunes as the option to sync with both PC and Mac appears in the iPod setting. This can only be changed by connecting the iPod to the PC and unsetting the option at the PC end. I can just see it deciding to automatically sync despite the settings and cocking everything up again.
PS. My grass is also now a foot high.