I'd phone Steve Jobs and ask him why iTunes and the iPod is such a restrictive pile of crap, but that's just me…
I was gonna say something along the same lines, but that won't fix this problem. I always firmly recommend buying music on CD. That way you will always have a hardcopy and get decent quality audio, not a fraction of the original audio files! With a CD you choose the quality and format of recording.
There is recovery software for the deleted files on your old laptop (just google delted file recovery). You must run this s/w immediately after deleting otherwise those deleted files are at risk of being overwritten.
If your files contained DRM tags, this may be why they didn't copy to the ext. drive. Again, get CD's and set iTunes to rip without DRM.
Apple Corp. really sucks! People still get seduced by the fantastic looks and UI. I too find myself attracted to these, but I just can't get my head round the incompatitbility issues, the lack of replaceable battery and things like being fleeced an additional £120 if just I want a player with an additional 8mb of storage! Why can't we have removable storage and replaceable batteries? Reason: profit! Apple treat their customers like rubbish, yet still people buy these products! I just don't get it. "Fashion victims" I conclude.