NO PAINT PENS!!
I paint as a hobby and I have painted on metal many times. With that being said, use the smallest paint brush(white tip preferred or the softest tip you can get) and touch up paint. Apply the paint in layers. After one layer, let it cure (dry) before you put the next on. This will help prevent it from looking uneven. Yes, this can take a long time but if you want it to look good without repainting the door....
Do the same with the clear coat as well.
If you can't do this is fine someone else that can because you can't undue it.
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