Is the 01-10-2006 updater safe yet?

Back when the 01-10-2006 updater came out, I was one of the people who had major issues with it. My iPod wouldn't connect to my computer; neither iTunes nor my computer would recognize it.
Two new iTunes versions have been released since then, and on a hunch, I plugged the iPod in, and amazingly, it worked. I did a complete system restore, since I had (or at least I assume it was me) corrupted many files on the iPod when I was struggling to get it to connect previously (pulling it out while it was still connected since it wouldn't stop trying to connect, etc).
The iPod is now plugged in to the wall, totally back at factory settings. My question is: with the new iTunes versions, is it safe to use the 01-10-2006 updater now? Or will I only have the same problems all over again if I stick it back on?
Should I put on the 6-26-2005 updater instead? My only problem with this is that the file on my computer (Start - Program Files - iPod - 6-26-2006) doesn't seem to work when I open it on my computer ("iPod Manager Internal Error"), but the one prior to that, the 7-15-2004 update, seems to be functioning. Can I even redownload the 6-26-2005 update anywhere else on the internet?
One last question - I have 8000+ songs for my 40gig iPod...will putting them all back on at once damage it? I've noticed it's become really hot when I put on 1000 songs at one time in the past.

I don't know why you were having a problem with 3 and 10.6.4. I had no significant problems with this combination, especially with the updates to 3. Now, with 3.1, things are much swifter.
I did have one problem, which you can read about at http://discussions.apple.com/thread.jspa?threadID=2620852&tstart=0. This was to do with my Photo sync using iTunes and my iPod Touch. This problem surfaced after I installed 3.1, but I don't know if it was related. In all other respects, 3.1 seems to rock.

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