Tiny sanding sticks are available for scale modeling which should work. If they work on scale models with sometimes much smaller details than that I'm sure it should be o.k. for the thruster cones. Check with your local hobby shops or an online hobby store. e-hobbies, squadron, ect.
You could also try self stick sandpaper if you can't find the sanding sticks. Just cut the size you need and stick it to a piece of wood a pencil or whatever you will use to get in there. My thrusters from the new version of that pack are like that as well. I might use the end of a small piece of wood to stick the sandpaper on. Or I might try using my new Dremel I just got.
You can also use small jeweller's files available at most hobby shops & some hardware stores. They come in all different kinds of shapes, round, needle, square, etc. The needle file is especially great for getting in those tight inside corners!