The ancient Inca city of Macchu Picchu

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The original sentence contains several flaws. First, the past perfect "had been" is unnecessary here because there is only one past event. Second, "high enough" implies that the oxygen deprivation was a goal of the Incas. Third, "it" in this context is ambiguous: is it the altitude or the city that makes tourists sick? Finally, "sick with" is incorrect. It should be "sick from."

(A) This choice is incorrect as it repeats the original sentence.

(B) This choice incorrectly uses the past perfect "had been." Additionally, the pronoun "it" is ambiguous in this context and the phrase "so high of an altitude" is awkward.

(C) This choice incorrectly uses the phrases "high enough altitude" and "sick with."

(D)CORRECT. The simple past verb "was" correctly replaces the past perfect verb "had been." The phrase "such a high altitude" replaces "high enough altitude." The sentence is rewritten to avoid ambiguity by removing the pronoun "it." Finally, this choice uses the phrase "sick from" in place of the unidiomatic "sick with."

(E) This choice incorrectly uses the awkward phrase "so high of an altitude." Additionally, the pronoun "it" in this context is ambiguous.

D is the answer.

A. had been built at a high enough altitude that it often makes modern-day tourists from lower elevations sick with oxygen deprivation (had is required only when there is one other incedent in the past that happens after it)

B. had been built at so high of an altitude that it often makes modern-day tourists from lower elevations sick from oxygen deprivation (same as above)
C. was built at a high enough altitude that modern day tourists from lower elevations often become sick with oxygen deprivation when visiting the city (sick from is the wrong idiom , also 'a high enough altitude' is awkward it should be used in a different context)
D. was built at such a high altitude that modern-day tourists from lower elevations often become sick from oxygen deprivation when visiting the city
E. was built at so high of an altitude that it often makes modern-day tourists from lower elevations sick from oxygen deprivation (it refers back to the city , as though the city makes tourists sick)