1.make train construction assembler not actually working:
by setting assembler` active is false,the assembler can become a container for holding the train,which keeps item data like equipments so you can access it when needed.
but if you really want to make it like working,you can still just controling the progress bar using scripts :/

2.make train construction actually using the fuel item in the recipe:
trainassembly.lua line 1146 you should be able to detect the item if it is a fuel that matching the fuel usage of the train...I mean it is so close to that...