Re: Location of main files
Assuming you don't have complete records of what you changed, you can find this out by downloading a set of the exact same version as you have installed, and comparing the files in that to yours. Any differences are your changes which you will want to keep.
You can copy those files into a new set of /your_template/ folders (making a complete custom template - see FAQs) and proceed with the upgrade. It won't matter that the original files were changed because they will all be overwritten by the new version's files. Only your template files will be carried over intact.
It is true that in some cases, starting from scratch will give a cleaner and better result than upgrading files which include first muddled attempts at doing certain things.
Re: Location of main files
Thanks for your reply. I'm all sorted now. I just bit the bullet and copied them all over on top of the originals.
I hadn't realised how many "tweaks" i'd done but after a few hours its all running great (touch wood!).
Thanks for all your help, you are a very helpful bunch of people!