Time machine remembers moved or dead drives

Hello.  I've been having a hard time wording this in typical searches, to get appropriate answers.
Here goes: I have a older Mac Pro with four internal drives. One drive, my boot drive, failed.
I had been using an external drive for my Time Machine backup. On that backup, I had included a lot from the other internals.
Once I had isolated the problem (the internal was dead or dying) I made room on one of the other internals by moving things around- condensing to allow for a Restore to one of those three remaining drives, temporarily, as I planned to buy a new internal and a larger external.
Suprisingly, it went great! I ended up with a perfectly restored boot drive with all my Apps, etc.
Now the problem:
When I turned Time Machine on, intending to create a newly restored version of my boot drive---to the new drive I just purchased, TM had a stored list of items that were spread out among the other drives, but I had moved these items all around.
I'm afraid to run TM at all now, not knowing how to tell it to ignore items, volumes, even drives; and restore only the boot drive with its applications etc., and not the various other items that were in places that no longer exist.
If this makes sense, and anyone can advise me, I will greatly appreciate it.

David Kerman wrote:
I just restored the first drive. My system drive. I keep all of my work on the other drive except for itunes, iphoto, and iweb. I initially restored from my latest backup. Same OS. No changes.
When you restored the second time, from an earlier backup, was that the same version of OSX?
I didnt do anything about my second internal drive. The mail message was just saying "welcome to mail" and then everything was okay. But this was still a scary sight. I didn't do anything crazy in the terminal, however i did used the CS3 Clean scripts from Adobe and I think that was the real cause of all this misery.
I don't know what that is or does, so can't advise on that.
Should i just restore EVERYTHING on both drives?
If you restored an earlier version of OSX, but had data in a newer format on the other drive, yes.
If the version of your boot drive that you restored has the Adobe applications, and the data was on the second disk, perhaps. Depending on what the "Clean Scripts" thing did, you may now have a similar mismatch.
If you're concerned about Spotlight indexing, don't be. Time Machine automatically omits some things, such as system workfiles, most caches, trash, and Spotlight indexes. So Spotlight will normally re-index a restored drive.
I don't know about the Quickview and Preview problems. What, exactly, is happening there?
OH, and yes. I just read that article. I did everything it said, however I ONLY backed up the first drive. Not the second
Do you mean you don't have backups of the second drive, or didn't restore it?
If you do have mismatches between the two drives, you may need to restore one (or both) again so they're from the same time.
and I was getting a ton of SUID permission errors that couldnt be fixed.
Are the SUID errors the ones shown here: http://support.apple.com/kb/TS1448 If so, you can ignore them.

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