Ouch! How many times have we made this mistake. The cause of this challenge is due to staining a sealed surface. Don't get me wrong, you did as you should have, It's the system which is misleading. You applied stain to the fiberglass door, but you did not actually stain the fiberglass. The stain was made to actually stain and absorb and on fiberglass this does not happen. The stain dries on the surface and usually a coat or three of varnish will protect it. That is until masking tape is applied.

As for your hopes of a touch-up. Yes, it can be done. No, it ain't easy. But then neither is stripping the door. Try the touch-up thing first. Follow the same steps for touch-up as original.

I am not sure I understand if the primer was also removed. If so, check in with your local paint dealer and get them to mix a primer close to the original color. He will suggest he can not guarantee the color to be perfect, this will not matter. Close is okay in this instance.