I have the exact same configuration! I went through the same thing when I hooked up the old computer's hard drive as an external drive with the iTunes library on it. I soon learned iTunes simply doesn't support that very well - a lot of web searches later I got a lot of my library back, but curiously not CD's I had ripped using iTunes into the iTunes library. Fortunately, I only have a couple of hundred CD's and a third party ripping program to convert to highest quality MP3. From there, I use a free program called "Media Monkey" to all my music organization. I now only use iTunes for the handful of songs I bought from the iTunes store, and may use audio capture for them as well. I used to use iTunes exclusively, but at some point in the past, they did away with the ability to transfer a single (or small group) of songs as I rip more vintage vinyl and tapes. They made it full sync, which is a pain the posterior because I don't need or want a time consuming full sync just for one song. Media Monkey adds that capability back, and I get exactly what I want - an file explorer type interface (that iTunes used to have). Eventually my goal is to have a very well organized folder structure of MP3's, and abandon iTunes completely except for buying songs. I already have a way to rip DVD's and transfer videos to the phone without iTunes - not that it had that capability anyway.
