Question

Which sectional economy was better prepared for war - the industrial North or the agricultural South?

Answer 1

I would go for the industrial North.

Explanation:

I would consider the Civil War as the first, large scale "mechanized" war.
In it, for the first time, large armies depended upon bullets, cannons, rifles, trains, railroads and ships to conduct offensive/defensive operations.

This goods were massively produced in the industrial North whereas in the South we had mainly agricultural monocultures of poor military value (cotton, tobacco.....).
The South had few factories or arsenals producing guns and ammunitions and even less shipyards equipped for the production of armed vessels (although the ingenuity of some southerners led to the development and deployment of the first operational attack submarine!).

A symbol of this disparity can be seen when the North, using its ships, imposed a blockade to the South strangulating the commerce of the agricultural goods of the South.