Sentence Correction

The first trenches 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 independently of the more
celebrated city-states of southern Mesopotamia, in
what is now southern Iraq.
(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
(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
(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
(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
(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

My doubt:

Option A

I understand that ..that parallelism is unnecsessary as well as wrong here
that---were cut..that were arising simuletaneously
Also it is unnecessary to use --that were cut when we can simply use CUT.

Apart from this please clarify isn't the placement of second that incorrect here.
The second that is placed --centrally administered complex societies in
northern regions of the Middle East that were
arising simultaneously with but

Isn't the second 'that' supposed to refer to the complex societies but is actually referring to Northern regions of middle east.

Please help.

Thanks