Just a couple of small comments:
Angus Pym woke up on the dot of six o'clock] Not a verb; but 'at six o'clock on the dot' would be more usual.
as he always does, no matter where he is or what he did the previous day.] The tenses here aren't incorrect; but they give a very 'vivid' impression. It might be more in keeping with the rest of the text to say 'as he always did, no matter where he had been or what he had done the previous day'.
that he was still wearing shirt and trousers,] 'wearing his shirt' would be more usual.
events of the previous evening was coming back to him.] not quite: you need 'the events of the previous evening came back to him'. (It's also quite common to insert a 'suddenly' in such contexts: 'suddenly came back...')
He had gone to his club for supper, had just finished his steak tartare and had looked forward] 'had been looking forward'
After an ice-cold shower, Pym was thinking carefully about] 'thought carefully about'
An hour later, as he was driving through ] 'was driving' is ok; but 'drove' might be better.
Pym was carefully considering the contents of the files.] again, 'was considering' is ok; but it puts quite a lot of emphasis on the process of considering. So you might want to say 'considered' instead.
All the best