Thank you very much for all the comments.
I was able to get the problem sorted out in the end.
First I used 'Advanced Find and Replace 7' to strip out all references to external domains and urls not in the directories I wanted. Then I used HTTrack to re-index the downloaded website that was on my hard drive. I did this twice to capture two different sets of Supreme Court case data - one set was from 1857 to 2008 and the other set was from 2009 - 2013.
I then combined the 'fol' and 'doc' folders from both sets and changed the code in the index page (that HTTrack creates) to reflect that. It took another day or so but the whole job has now been done.
I now have everything the way I want it AND I have the original database too! So that's neat. Mind you, the total size of these two databases is around 54GB!!!
Sorry I didn't re-post the screenshots I took, but I was so disheartened by losing the post that I couldn't face doing it from scratch again and just got on with trying to figure it all out by myself.
By the way, a weird message came up when I tried to post the original post. When I got logged out when clicking submit, it came up with the login page but when I tried logging back in it said something about not being able to log me in because I was logged into a post !!??? I can't remember exactly what the words were. But it told me to press the back button which I did and I tried logging in again but it didn't work. I knew that with the first failed login that I had lost the post so gave up after that.