Is it legal to make custom ponies?  Will I get sued for copyright infringement?
People have been making customized Barbies and Beanie Babies for years...I've never heard of any lawsuits.  Hasbro has not issued an official stance, as far as I know.
However, I have heard of auctions being pulled for infringement on other copyrights, such as the Harry Potter & the Lord of the Rings ponies.  These ponies were clearly not authorized by the respective copyright owners.  Still, a lot of people continue to make these ponies.  
Also, please make sure you clearly label your pony as a CUSTOM.  I doubt Hasbro would like it if you tried to pawn off your custom as an Hasbro original.

What about making a pony based off a Hasbro one?  Like a baby for an existing adult?
This is a gray area.  I don't think it's legit, but a lot of people still do it.  I won't make ponies which copy Hasbro original designs.

What about replica ponies?  I'm doing a favor for those who can't afford a real Greek Ladybird or Rapunzel.
This is probably a bad idea.  People have had their replica auctions pulled from eBay.  It's a long shot, but your custom may fall into the wrong hands and get passed off as an original.

What about creating one of these ponies for personal use?
As long as you don't display a picture of it or sell it, who is going to know?  That's between you and your higher power. ^_~

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