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The instructions in this exercise are 'put the verb in brackets...':

Exactly how these stones were transported is unknown. One theory is that they were brought naturally by glaciers during the Ice Age, but until recently geologists considered this impossible. Instead it .....(think)..... that the four-ton stones were transported by man using rafts to take them across the sea and up rivers.
It is obvious to any visitor to Stonehenge that building it without modern machines .....(not/be)...... easy, so why did they do it?

The answers in the key are the following:
1. is thought
2. wouldn't have been

Would you accept the answers below?
1. was thought (by geologists until recently)
2. would be (they did NOT use MODERN machines, so how can we speculate about the past here?; if people tried to build it without modern machines NOWADAYS, it WOULDN'T BE easy)

Thanks in advance.
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Your alternates are not really awful; it's just that the answers in the key are a little bit better. ( Emotion: sad )

"Instead it was thought (by geologists until recently) that the ... stones were transported by man..." is actually not true according to what precedes, which says, "until recently geologists considered [it] impossible [that the stones were brought by glaciers]

The contrast (shown by the word "instead") is between what was thought (stones transported naturally) and what now (instead) is thought (stones transported by man).

"building it without modern machines" has no tense to give us a clue, but "why did they do it?" does give us the clue that we are thinking of this from the point of view of the past and from the point of view of the people who built Stonehenge, not from our own modern point of view.
Another point to consider is that "building it without modern machines" implies parenthetically "which is how they did build it". That's a bit of a clue as well -- admittedly not a really obvious one.

With at least some clues that the point of view is the past, the preferable solution is "would not have been" (or "wouldn't have been").

This may be a disappointing answer for you, but I hope it helped.
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Thank you for your answer. However, I still have some doubts.

1. If (until recently) geologists didn't believe in the glacier theory, which they now consider plausible, they must HAVE HAD another theory - so can't we refer to the past here?

2. If the point of view is the past, how would you complete this sentence:
It wouldn't have been easy IF they ................... (had built it without modern machines??? - but we know they built it without modern machines!)
In my opinion, a possible sentence would be:
If they had built it WITH/USING modern machines, it would have been easier.

Am I still wrong?

Best regards.
On rereading the example, I am now inclined to say that your alternate "was thought" may actually be better, although I see nothing really incorrect with either.

As for

If they had built it WITH/USING modern machines, it would have been easier.

I'd say it's perfect.

"... building it without modern machines would not be easy, so why did they do it?" may be considered borderline acceptable because we sometimes make this substitution of tenses. Nevertheless, I still hear "would not have been easy" as 'more correctly placed in time'.

I hear the following as the correct sequences of tenses:

NOW: "Building the house without the proper tools would be difficult, so why should they do it?"

THEN: "Building the house without the proper tools would have been difficult, so why did they do it?"

There can certainly be differences of opinion about this, however.