Over crowding can stunt growth, but it causes internal damage as well. The delay in development is likely due to the stocking numbers in your tank. Platys do have the ability to be dimorphic, which means that female fish can turn male later in life. This most often happens when the ratio of fish is primarily female or if an only male dies or is removed. It is nature's way of preserving the species. That could explain the late change in your platy.
There is a lot of debate about how best to euthanize a fish. My preferred method is still to freeze them in a small zip lock bag of tank water. The gradual cooling water temp causes them to get lethargic/sleepy and then they just don't wake up. If you use this method, let the fish stay in the freezer for at least 12 - 24 hrs to be sure they are completely frozen and not going to "wake up" once they thaw out. The whole baggie can then be thrown in the garbage.
Be careful if you choose to use clove oil, which seems to be the preference of many lately. Clove oil is very potent, and if other fish are exposed to it, it can cause death quickly. Clove oil is also very difficult to remove from containers, so be sure to use something disposable and to bleach repeatedly anything that you intend to reuse, until all odor of the clove oil is gone. I use clove oil during surgical procedures on fish, and because of its potency and difficulty in removing from any surface, I have tanks that are designated for that only. My last attempts to bleach a 10 gallon tank that was used with clove oil, took me 6 tries with straight bleach, drying between each, and I still was not able to remove it all. I finally gave up and cut my loss of the tank and returned it to my group of surgical tanks. As difficult as it was to remove from a glass tank, a plastic container is even harder. Also... use gloves while using clove oil, and be sure to use enough of it and to leave the fish in there long enough... you would need to watch for gill movement and time it 30 minutes after all signs of gill movement have stopped. For small guppy fry it shouldn't take much of the clove oil to do the trick but leaving them in there long enough will still be important.
The only other thing I can suggest for you is to get a much larger tank if you decide to continue breeding these fish, and plan to separate them as I mapped in my previous post. If you wish to cut down population naturally, allow the female fish to live in the community tank and thin out the decorations when you are expecting fry. This will allow the other fish to eat the fry, which they will do if they find them. Even the female will eat them if she can get to them.
Good luck to you.