Thor's Cave is one of a whole series of caves in the Manifold Valley which is in the beautiful Staffordshire Moorlands. The Peak District National Park covers an area that spans parts of three counties Derbyshire, Staffordshire and South Yorkshire.
The only part of this film that I am definitely certain was filmed in Derbyshire was the hospital laboratory scene which was filmed at the pathology lab of the old Derby City General Hospital.
I have now added all of these locations to the filming locations section for this film.

Sparks Moran: "It was dusk. I could tell 'cause the sun had gone down"

It's called Stockers Farm and it's in Rickmansworth about 20 miles north west of London. It's the same farm from Xtro, Black Beauty (TV series), Children Of Men and many others.

I think the actual location in Manifold Valley is Monsal Dale.

I've also seen listings for Thor Cave being in the Manifold Valley, but in Staffrordshire. I'll just let it go at that, as I'm not that cognizant of English geography.
Of course, the film is fictional, and most of the story was not filmed in Derbyshire, but if the film was factual, and the story had taken place in Derbyshire, I figure it would most likely have taken place in far north Derbyshire. Something like this.
Friday, March 18
And the date can be gleaned from the newspaper James (Grant) is reading on the plane. Kevin (Pitt) after school, leaves Sheffield and takes the bus or train to Hattersage, where he stays overnight in the youth hostel.
Saturday, March 19
He sets out and hikes to Langsett, where he stays overight in the youth hostile.
Sunday, March 20
Then, after church, he sets out and hikes toward Crowden-in-Longdendale, or Longdendale in the film. He comes within two miles of the village, when he is picked up by Sylvia (Donohoe) in her car.
Now, of course, he did not make it to the village, but if he had made it, he would have stayed overnight in the youth hostel, and then . . .
Monday, March 21
He would have taken the bus back to Sheffield.

I think Thor Cave is in the Manifold Valley in the Peak District Derbyshire.Went there on a school trip in the 80's!

Since Gaddesden Place, which was the stand-in for Temple House, and Knebworth House, which is the stand-in for D'Ampton Manor, are both in Hertfordshire, I'd say that most of the film was filmed in Hertfordshire.
Now Thor Cave, which was the stand-in for Stonerigg Cavern, was in Derbyshire, that part of the film was filmed in Derbyshire.
The scenes at Mercy Farm, which I have never been able to locate, may have been filmed in Derbyshire.