All my preferences suddenly missing? Mail,iTunes,Firefox etc Mac OS X 4.11

Hi there,
I own a lovely 7 year-old MacBook Pro, still running OS X 4.11. Before you laugh at me for not upgrading it has worked like a dream and never felt the need to upgrade though am sure I'm missing some good things by not doing so.
Anyhow the other day, down to about my last 6 GB on my internal hard drive (87GB used of 93GB), my Mac Mail started misbehaving and asked me to restart.
On restart, my whole desktop, icons/thumbnails etc were all jumbled beyond recognition, sidebar was almost empty, Mac Mail when opened asked me to start from the beginning (i.e.set up an email account etc etc). I did this, because I could remember the settings for my addresses. Then Mail asked me to import my old mailboxes, which it did - but everything looks different, fonts, no signatures (they'd taken ages to organise) and no inbox or sent meail folders.
Ditto Firefox and Safari - when opened, all bookmarks have disappeared, and all autocomplete passwords for sites have gone.
It's clear my system is pretty messed up. Luckily, I have a bootable Carbon Copy Cloned external drive of how my Mac used to be 6 weeks ago. When I used this to boot, everything above was back to normal.
My questions are:
1) Is there any way to get back to where my system was before the blowout using my Cloned Drive? I.E. Can I simply erase the contents of the internal drive and 'paste' over it with the Cloned Drive? Is this risky?
or
2) Is there a less invasive way - is it easy to reintroduce the old preferences from the Cloned drive?
finally
3) Do I need a new hard drive?
Any help would be much appreciated.
Thanks!
Adrian
System
Model Name:          MacBook Pro 17"
  Model Identifier:          MacBookPro2,1
  Processor Name:          Intel Core 2 Duo
  Processor Speed:          2.33 GHz
  Number Of Processors:          1
  Total Number Of Cores:          2
  L2 Cache (per processor):          4 MB
  Memory:          2 GB
  Bus Speed:          667 MHz
  Boot ROM Version:          MBP21.00A5.B08

PS OS X 4.11 doesn't have Time Machine, so that won't work....

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