If you are wanting lineside photos rather than riding on/ stations then get yourself an os map, there are loads of footpaths that seem to follow the line, it's a long line though so would be a very long walk.
Have never photographed the ffestiniog so can't recommend any locations personally but where it crosses the estuary at Porthmadog and the spiral at Dduallt are well known spots.
Have you looked on Flickr to see if you can work out any of the locations?