The state highways historically ran from north to south, because that orientation fit the patterns of the existing cart paths through the mountains, but they were later diverted toward the coastal cities, often looping around the suburbs before terminating either in downtown transit centers or airports.
A. The state highways historically ran from north to south, because that orientation fit the patterns of the existing cart paths through the mountains, but ---
The correct choice.
B. Historically, the state highways ran from north to south, because that was the orientation of the existing cart paths through the mountains, but – the standalone demonstrative pronoun has no proper referent
C. While state highways ran from north to south historically, the orientation of the existing cart paths through the mountains, The underlined part is a fragment with no verb for the main clause. Wrong
D. Because state highways historically ran from north to south, since it is in the direction of the existing cart paths through the mountains----The couple of subordinate clauses do not have even one single main clause to fall back on. Wrong
E. State highways, beginning by traveling from north to south, because this is the direction of the existing cart paths through the mountains –The subject state highways has no verb
A is the best choice.