My pick is "E", please find rationale as under:
A. that were cut into a 500-acre site at Tell Hamoukar, Syria,
have yielded strong evidence for centrally administered complex societies in northern regions of the Middle East that were arising simultaneously with but
After "have yielded strong evidence" "that" is require to start a new clause bcoz "centrally administered complex" is a subject of the next clause.
B.
that were cut into a 500-acre site at Tell Hamoukar, Syria,
yields strong evidence that centrally administered complex societies in northern regions of the Middle East were arising simultaneously with but also
"that were" - Plural and "yields" - Singular both have subject "trenches" which is plural.
C.
having been cut into a 500-acre site at Tell Hamoukar, Syria, have yielded strong evidence that centrally administered complex societies in northern regions of the Middle East were arising simultaneously but
"having been cut", which modifies "trenches", is a wrong usage of perfect participle. A correct usage would be "having cut"
D. cut into a 500-acre site at Tell Hamoukar, Syria,
yields strong
evidence of centrally administered complex societies in northern regions of the Middle East arising simultaneously but also
"cut into a .." is a correct usage of "Past participle modifier" however, "yields" suggests "trenches" as singular" and "evidence of centrally administered" does not serve as a subject of following clause.
E. cut into a 500-acre site at Tell Hamoukar, Syria, have yielded strong evidence that centrally administered complex societies in northern regions of the Middle East arose simultaneously with but
clear, conscise and grammatically correct.
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