Wow, I’ve never seen so many stacked gear assembles before. If you are going to do this a lot then the small washer between gears will help. For the ones you have spray some WD40 on the shaft and let it soak down the shaft.
From the pictures it looks like the shaft has twisted.
You could try placing the stack (big ones down) on a flat surface with a small hole in it, just a bit bigger than the shaft. You could drill a hole through a board to accomplish this. Then use another shaft or similar along with a hammer like a nail set. With the tapered ends of the shafts, each time your “nail set” gets into a given gear, that gear should be easy to remove from both shafts. You should not have to strike the “nail set” very hard, so you should be able to avoid damaging another shaft.