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I'm trying to understand why in this sentence from a book I'm reading the past perfect is used instead of the present perfect:

For a long moment he thought he had gone too far.

vs

For a long moment he thought he have gone too far.

CGEL has these examples in Chapter 3:

He was believed to have written it the previous week

At that time I had written four chapters.

In both, the perfect locates the writing as anterior to some To which is identified via other features of the sentence as anterior to Td

In my example, why is 'he thought' not enough to locate the To in the past without using the preterite perfect? Thanks.

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    Because his going preceded his thinking. The present perfect connects the past act to the present. The past perfect connects the earlier past act to the past temporal origo. He thought .... he had gone. He thinks...he has gone.
    – TimR
    Apr 17, 2017 at 13:32
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    He fears he has eaten a poison mushroom. He feared he had eaten a poison mushroom.
    – TimR
    Apr 17, 2017 at 13:39

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For a long moment he thought he had gone too far.

The present perfect of this would be "he thought he has gone too far," by the way.

He thought X means he thought X in the past and can also mean that now, he is no longer thinking X.

So, if we express X in the present, it won't make sense because of that contradiction.

You might think that because at that time in the past, he was at that time "now" thinking X that the present tense should be used for X. The problem is you are strongly implying that he later realized he didn't go to far. So that thought also is in the past and not still true/relevant to now.

I think your only other option in English if you want to express a thought that had occurred in the past like this with a "now in the past" is to use one of the modals may, might, must, would, or could:

For a long moment he thought he may have gone too far.

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