Door hinge & plate

I made a research and I find useful information, but I still have some questions. I read this webpage: http://www.desertmustangs.com/1972coupe/Hinge-Rebuild/72-Door-Hinge-Rebuild.htm

but I find that the pins I have (new ones and old ones) doesnt have a "top hat", just the ordinary flange, 1). is that something you need to buy in a hardware store?
Top Hat:

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2). does the flange goes on the bottom or top of the hinge?
Pins and bushings I get from NHPony:

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while taking a hinge from the door, a rusted screw broke inside the plate,
3). do I need to dissamble the door to take the plate out and then drill out the screw?
Pic of the broken screw:

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