Learn English – What does “notwithstanding” mean in this sentence

Consider these notes on dealing with reported speech containing the word ago:

Changing time and place references - EducationFirst:

• Phrase in direct speech: "I saw her a week ago," he said.
• Equivalent in reported speech: He said he had seen her a week before.

Time and Place in Reported Speech - English Club:

• Direct speech: two minutes ago
• Reported speech: two minutes before

Noun Clauses/Reported Speech (Indirect Speech); Tense Harmony or Sequencing - Mary Nell Sorensen, University of Washington:

• Direct speech: five days ago
• Reported speech: five days before, five days earlier

Cambridge Dictionary

• Direct speech: ‘I finished the job three weeks ago,’ the boy protested.
• Indirect speech: The boy protested that he had finished the job three weeks before.

The last reference also provides a rationale for the shift from ago to earlier or before:

We often change demonstratives (this, that) and adverbs of time and place (now, here, today, etc.) because indirect speech happens at a later time than the original speech, and perhaps in a different place. - Cambridge Dictionary

This accords with the normal use of ago as a time reference based on the speaker's present. In reported speech, the speaker changes, so the word ago no longer conveys the correct time. The word ago is therefore changed to earlier or before.

On this basis, the word ago in your example references the present (time) of the speaker of the sentence. Since you indicate that the full sentence was uttered in 2016, the time two years ago refers to 2014. This is so even though the sentence reports a traveller who spoke in 2015.

First of all, the information available does not lead to your conclusion that Jefferson is "not sceptical, and he is enlightened."

In your incompletely quoted sentence, the pair of linked adjectives 'skeptical but enlightened' work together to describe the noun 'intellectual' -- the meaning would be that 'the intellectual in question is skeptical; however (he) is enlightened' as in 'being skeptical doesn't prevent (this intellectual) from being enlightened', to expand the meaning.

The word 'but' as used here is unrelated to 'far from' as used at the beginning of the sentence.

Since the second half of the sentence is not quoted, quite a little context is missing, but 'far from' is usually used to mean 'does not do', 'does not mean to' 'does not intend to' or 'disagree' as in 'it is not (my) intention to view Jefferson as a skeptical but enlightened individual...' or 'I disagree with the way some people view Jefferson as a skeptical but enlightened individual...' as pointed out by the learned members in comments.

Moreover, 'far from' implies the meaning 'not that, but quite the opposite' where there is no need to explicitly state 'but', since it is usually implicit in 'far from'.

Other examples:

Far from praising the student's efforts, the teacher strongly criticised his lazy work.

Far from holding him up as a fine, upstanding citizen, I consider him an unmitigated scoundrel.

Note: but is used in the same sentence as far from only to suggest some mitigation, and only in a more complex construction such as

far from praising his efforts, the teacher criticised his lazy work, but agreed that his basic argument was valid.

Note 2: As the member has mentioned in comments,'far from' is also used in the sense 'not at all', 'insufficiently' or 'not really' as in "they were far from pleased with his sneaky trick", "his explanation was far from satisfactory" or "his answer was very far from the truth."