Music not playing. Corrupted files?

Ok so my library exists on an unjournaled external drive. I got another one to accommodate my video collection and left the iTunes library on the original HDD. After a few days of HDD maintenance (longest being defragmenting, which I did more than once in the time frame) on all 3 of my drives all data was in great shape. Later I ran into an error, my eDrive would mount and unmount constantly and I couldn't eject the drives. I proceeded to shut my computer down. The new HDD (without the eDrive) successfully ejected upon shut down, the second remained completely on, spinning and everything. Normally the drives power off when ejected and then I hit the power switch. I reluctantly turned it off. When I rebooted I ran a check for corrupted data, one unimportant image file was corrupted. Not bad. Later I found a 1.8GB (ish) game would not open and asked to be reinstalled. I did so and lost my character data, oh well. Now I find that chunks of my iTunes library (no podcasts, just music) are not playing. Those chunks I would consider localized as they remain in the albums. When playing through, iTunes will simply skip the tracks and go on to the next playable one. I reveal the file in the Finder and attempt to open it in Quicktime and it is not a file that Quicktime understands (-2048). So what is here? Even after syncing the files are still on my iPod, should I delete them from iTunes and use Senuti to get them back? Anything is welcome.
Bonus points to anyone who can tell me if there's a way to prevent iTunes from automatically syncing my iPod on connection. An example of what I mean is I hold a key as iTunes launches to prevent the sync.
Thanks,
Alex
15-inch 1.5GHz PowerBook G4   Mac OS X (10.4.4)   1.280GB RAM, 128MB VRAM

Thank you very much!
And to anyone else, I've found that some corrupted files have made it to my iPod. It just skips them and continues. I have yet to find out if it is growing, and if it is I have some paranoia theories.
1. Modern Mac Virus (But the last Mac virus would of been released before iTunes it's been so long, it couldn't be)
2. iTunes corrupts songs that are not purchased from the iTMS
3. The RIAA has a virus that spreads to computers without copy protected music
I doubt my defragmenting harmed it. Luckily I can just get my music back, but it's a time consuming process and something I shouldn't have to do..
Alex.

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