The skill and the precision of the Anasazi, ancient inhabitants of the Southwest,
in measuring the movements of the Sun and Moon is evidenced not only at Chaco Canyon but at a number of other sites.
First split - SV Agreement. The Skill and The Precision = compound subject, therefore plural "are" is required, otherwise we are evidencing one, not two, things.
(A) in measuring the movements of the Sun and Moon is evidenced not only at
(C) in measuring the movements of the Sun and Moon is evidenced at not only
(D) to measure the movements of the Sun and Moon is evidenced at not only
I have a hard time rationalizing why I selected B, so if not a difference of idioms, E also implied to me that The skill and precision are TO achieve something. What is that something? To measure.....
Idiomatically, "the precision in his craft", "the precision of his measurement" --both correct, but "the precision in measuring..." seems incorrect since the precision is in the measurement itself not TO measure.
(E) to measure the movements of the Sun and Moon are evidenced not only at