Does software for optimizing the train route in 18xx systems exist?
Not to my knowledge.

One thing I've done to assist with this problem is to use a pile of D6's of a couple different colors.

Place a D6 on each city of one color to represent your smallest train and work your way up to your largest.

When you are finished, pick up the D6's generating your total run profit as you go.

Towards the end of the game, we usually help each other, as the diesel runs can become quite dramatic as I'm sure you're aware!  It just speeds the game along as we don't want one person obsessing over his run for twenty minutes to gain an extra $10.