Not loading correct startup prefs (safe mode?)

Trying to rebuild my system after a hard drive failure (backup on external drive was somehow corrupted as well). Luckilly, my ipod contained all my music (although I did lose all movies and TV shows) and was up to date.
I have my new system configured with my Home directory on it's own volume so that my data is separate from OS. I have Time Machine backing up my home directory and a clone of startup volume---both on separate physical disk (so that if primary disk fails, I'm instantly back-in-business)!
So I executed the Terminal script necessary to access hidden files, and was able to copy all the music back to my system using seruti (or whatever it is), and was in the process of copying all the playlists I had sync'd ... but I couldn't copy them because iTunes kept automatically launching when I connected the iPod, and therefore preventing Seruti from maintaining "control" of connected ipod (which is the only way it can "see" what's on the iPod). So I went into System Prefs to disable iTunes Helper from default startup items... but when I logged back in, both Microsoft Daemon and iTunes Helper were gone from the list, and then when when I rebooted, ALL my preferences were gone. Wallpaper, apps in the dock -- it didn't even prompt me to login.. it just went straight into an account with no previous history (asked me to agree to iTunes EULA).
Thank god I have a clone of the startup volume... I booted from that, and everything was okay. Interesting thing is, Advanced Settings for my account are same on both volumes -- reading from my Home directory on that separate volume. Or... at least, one would think since the path is the same on both volumes. But logging into each produces different results.
Can anyone shed light as to what happened, and how I might go about fixing it?
It just ocurred to me to mention that I - per an instruction I read regarding the process - to hold down Command + Option when connecting my iPod which would prevent iTunes from automatically syncing. However, I was still prompted, but saw a message that iTunes was launching in Safe Mode. Does that mean that the OS on my primary startup volume is launching in Safe Mode, but the one on my clone is launching normally? It would certainly explain why it loads fine from one but not the other given that account settings are same on both.
If that IS the case, how do I disable Safe Mode?
Many MANY thanks in advance!!
Message was edited by: dotScot

I called AppleCare... the first guy I spoke to left me on hold for quite a while after he finally understood what was happening. But when he came back on, we got disconnected, and he never called me back (even though he asked for my number when we first started talking).
I called back, and explained everything to the second guy... who, brought more to the table from a troubleshooting perspective, but was ultimately unable to figure it out, and said that I'd have to call back tomorrow and start over because his "product specialists" were gone for the day, and he wasn't able to create a ticket for such a unique problem.
Wow.
I haven't felt this beaten down in quite a while. Isn't there anyone out there who can shed some light? I don't really have time to spend another 3 hours on the phone.
What's interesting now is that, even though I'm trying to copy my Home folder over to the primary startup volume, and I've set permissions "read/write" for everyone.. it still won't let me copy -- says I don't have permission.
This is soooo frustrating. Everything was fine until I started dorking around with it in an attempt to recover music from my iPod because Apple hasn't figured out a way to cover their ***** from a Digital Rights Management perspective while still allowing users a way to recover their music in such a scenario.
Now I don't know what to do. Do I rebuild from scratch and just bit the bullet on having OS and data on same volume? Maybe this is how I have to do it:
_*Physical Disk A*_ (500GB)
- Partition 1: System - 220GB
- Partition 2: TimeMachineClone - 220GB
- Partition 3: Downloads - 40GB
_*Physical Disk B*_ (500GB)
- Partition 1: SystemClone (Bootable) - 220GB
- Partition 2: TimeMachine - 220GB
- Partition 3: Scratch - 40GB
_*External Disk*_ (250GB)
- Partition 1: TimeMachineClone

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