How am I supposed to pick up the wagons/train engines? Thanks

You can't, it's part of the challenge :)
You can however drive them (hover mouse over vehicle and press enter), so you can move them out of the way.
Preferably you wouldn't be able to carry vehicles at all, but then you couldn't place them either.

I love your mod, starting to set my railworld, and was going to ask the same thing : if a train accidentaly falls out of fuel, how can you take it away ? We're even unable to erase it. We should at least be able to use the deconstruction tool, no ? And I believe it's the same for cars.
I ask it because as you can understand, I have a train stuck in the middle of my railroads, and I can't do anything. I could set new rails around it, but it seems a bit weird as solution.
Another question, related : if I want to change the size of a train (ie take away 1 wagon or replace a wagon type), how do I do ?
Tks for your answer :-)

You can connect/disconnect locomotives and wagons using the "g" and "v" keys. So if you've stranded a locomotive, enter another locomotive, drive up to the stranded locomotive and hook it up, then tow it to the nearest refueling station. Resizing trains is similar, enter wagons and press "v" to split the train into two parts :)

Oh ! Tks a lot for the tip, I'll give it a try, should be fine :-)

thanks! been enjoying the scenario.