Unresponsive iMac

Our iMac (iMac 8.1, purchased about 1 1/2 year ago, running the latest update of MacOS 10.5) started to act strange (slow response, lots of waiting etc.) a while ago, but I blamed my wife for having too many icons on the desktop and too many open tabs in Firefox.

However, things turned to the worse the other day, becoming almost completely unresponsive (the mouse pointer can be moved, but icons on the desktop and the Finder menu-bar appears after several minutes since the dock has appeared). At first I thought it was Spotlight indexing, after having its index files damaged or something, so I made it re-index and left the computer on all night, but that didn't help. I also tried checking what's hogging the computer by running "Activity monitor", but of course that application (like all other apps) take about 5 minutes to start after clicking the dock icon, so when it finally runs whatever has been hogging the iMac is done.
I've also tried booting from the system DVD, then running disk utility to check the drive (no reported problems) and checking/repairing permissions (this does tell me some permissions needed to be fixed, but unfortunately didn't help after rebooting).

I've also tried to "archive and reinstall" the operating system with no improvement. What else can I try?
I would think completely wiping the drive and reinstalling everything from scratch would do the trick, but that would leave me with a lot of work putting personal stuff I want to keep back into their right places (email (Apple Mail), bookmarks, passwords and web history (Firefox and Safari), Address book entries etc.).
I have an external Firewire drive connected to the iMac which does Time Machine backups regularly, so I shouldn't risk losing anything, but just restoring from that drive could mean I'd just put the problems back in, wouldn't it?

Finally I tried creating a new user, to see if the problem lies within the user folder, but right now I can't even change to that user because the iMac boots directly into the regular user and there's no response when clicking on stuff. If the iMac does start responding I'll go into the "Accounts" system preference, turn off automatic login, reboot and log into that fresh, new user and see what happens. Until then, what do you guys think is the reason behind all of this, and what should I do?

 

It's hard to pinpoint if it's temporary or permanent. It seems to change now and then. I looked in the console, but it's way too complicated for me to understand.
I think the best solution would be to back everything up (I assume my latest Time Machine backup will do), wipe the hard drive and reinstall MacOSX from scratch, reinstall the additional applications I have, then put the user documents and files back. In other words: I would like to avoid keeping as much as possible when it comes to replaceable files (which includes most user-settings I suppose), but of course put back the irreplaceable files.

The only problem is knowing which files/folders contain my mail, bookmarks, address book data etc within my backup. Is there an application around which will easily find those files and install them on top of a fresh MacOSX system, or do I just need to figure out where they are and drag them over from the backup drive? In that case, where are the following user-files located?:

- Apple Mail's email account settings, email messages, attachements etc.
- Safari's bookmarks and passwords/usernames
- Firefox's bookmarks, sessions and passwords/usernames

.... plus anything else I might have missed?

 

I've spend a while trying to do a final Time-Machine backup before reformatting the iMac hard drive, but with more or less unresponsiveness (it seems that even though things start responding again like the Finder desktop getting all its icons and letting me click on a dock application etc. then the computer becomes unresponsive again when I give it something new to do)... it looks like I won't be able to make any more backups. I even tried logging into the different users and creating a new one. Didn't help.

Hoping that I could boot into MacOSX with the system DVD, then somehow making a backup on to my external drive but seeing that it's not possible I tried something else:
I hooked up another external hard drive, booted with the system DVD, installed MacOSX on to that external hard drive, then rebooted with the same drive. Now I have MacOSX working, so I should be able to make a backup from the iMac's internal drive on to the Time Machine external drive (where I have all my previous backups as well).
But it doesn't seem to be possible to back up from a different drive than you boot from -are there tricks around this limitation (of course without overwriting my existing Time Machine backups from the past few months)?
Are there other smart ways to make a backup of my iMac's internal hard drive before I reformat it and reinstall MacOSX from scratch?

Again, if someone knows a good way of transferring all my personal files from the backup on to the iMac internal drive again, without bringing along all the unnecessary stuff that I'll either reinstall (various applications) or redo (most preference files), please do tell.


PS: meanwhile, I'll just copy the "User" folder over to one of my external drives as a preliminary backup. I bet Time Machine copies over hidden files and such which a normal Finder copy procedure like this won't, but I should still get to keep all my files, right?

 

An update....
It looks like the iMac internal drive is either partly malfunctioning hardware-wise, or it's so messed up software-wise that nothing will fix it. Still, I find it very strange that "Disk utility" tells me the drive is OK when I test it, and using "Onyx" I was told that the SMART status was OK

I gave up backing up with Time Machine when having booted from an external drive because it seemingly doesn't have an option for backing up anything but the drive you boot from. So I tried simply dragging my user folder over to the backup drive, only to experience that it would stop after a while saying it couldn't copy all of that folder or something. I should probably have paid better attention to see if I got some specific error messages, but all I can remember at one time at least is a -36 error code. I also tried "Carbon copy cloner", but that also resulted in failure.

So next I tried a little experiment, to see if the computer itself seems to work or if it has something to do with the internal drive (or drive controller): I tried copying files between the two external drives, which actually worked fine! Once I reformat the internal drive it remains to be seen if things work like they should after a fresh MacOSX reinstall...

I have one question when it comes to restoring my backup data:
What's the best way to restore things from a Time Machine backup? Will everything be copied back the way it was backed up, or can you choose what you want restored, then eliminate the rest?
I'm asking because I only want to restore irreplaceable data like my documents, email and web bookmarks, but want to leave out anything else which could be the source of my problems in the first place (corrupted preference files, plugins, libraries etc.).