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Restore Mode and much more

Update:12-10Source: network consolidation
So, I am having a ton of trouble with my iPod recently. I had outlined my first problem in an earlier thread <>.
No one was of any help there, but now I have some new problems. Eventually, I was able to restore my iPod on an XP machine, and it started to work fine on my Windows 7 machine. I would press the sync button, and it would take for ever on one song, and eventually just stop for no reason. I would press the sync button, and it would start and eventually in this stop start syncing process it would give me an unknown error (-69 and -40). After restoring it a few times and trying again I eventually got it to get a few thousand (out of my 12k) onto the iPod and just gave up until the morning. I had left it playing and it eventually died.
I plugged it into my computer (Windows 7) in order to charge it again, but it gave me an error that it was in "Restore Mode" and needed to be restored. Then it gave me an error that it was unable to restore. I did everything on the list as well as reassigning the drive letter to an unused drive etc. I can't restore it, I can't do anything with it. Windows can't even format it at all. Any help would be wonderful.

The Best Answer

Maybe I didn't phrase the question clearly. Why did the simple online update (I don't know all what was updated; there's no log to show what was done...) basically zero out/reset all my applications. My fonts are gone as well.
I do still have my working docs as they were on different hard drive from the system and applications. I have email, Firefox bookmarks, fonts, etc. on my old machine, so in a sense, all I lost were 5 days worth of emails and time spent pulling my hair out.
I just want to know what I might have done wrong in the first place to cause this. Just don't want to do it again.
Mac Pro 1.1 Mac OS X (10.4.7)