Thanks for all the suggestions. I picked up a 3/8" rod which was 36" long. since I will be using the GarGraves Gantry Crane track which is 37" long.
I think for my first try at this I will go with the rod on top of the train table. I just need to get the motor and make a control box and find a bracket to attached the nut to the rod.
And I do like the idea using another side track with the engine pulling the gantry crane.