Currently, the entire rail transport capacity of the South (let's say 90 pts) can be available during one turn (15 days) deep far away in the Texas. That same totallity of the nation mobilized locomotives and train can be immediatly available 1 turn after (so 15 days after) in the completely opposite side of the country, let's say in north Virginia.
The same for the Union.
This is absurde and unrealistic.
I don't know if it is easy to implement, but i would suggest, instead of having only a big rail transport value for all the country to fix at the begining of the games or scenarios a value for each big region of the map (like the "naval region" scale for example).
Then you can buy more rail capacity for each region separatly.
Then you can also transfert a part of this capacity but only to one theater close to a another... and only if there is not dynamited lines cutting the links or if there is naviguable river links to transport the locomotives.