You have, dae exporter is default in Blender. Misaligning happens usually when origin is not set properly, origin of all parts need to be 0,0,0 and then you need to hit ctrl-a and apply location, then do second time and choose apply rotation and scale. You have to do this for each part of train in blender, walls, roof etc. Also your mesh names need to be setup into flexbodies section as each of part is own mesh, like walls and roof etc. There is also offset, which overrides applied location and rotation, but it can get hair pulling, so usually it is good to avoid that, check out documentation here: https://wiki.beamng.com/Flexbodies https://wiki.beamng.com/JBeam_Reference#flexbodies
