So your father owns the two sites, you funded the building of a house on one. Is this right?
I dont understand why your father didnt transfer the site into your name, as who ever owns the site, owns the house, regardless of how the house building was funded.
Its very difficult to give advice on this, as we dont know when the house is to go into your sisters name- and things may be different tax wise at that stage.
If it were to happen now, I suppose you would just do a deed between your father and your sister, which depending on the value of the site, should be exempt from CGT, stamp duty and CAT ( if its her first house and site and she intends to live in it as her PPR and if the house isnt fully built) and then you would do a deed of trust saying that you funded the building of the house and she is to pay you back. If the house is fully built, then its no longer the transfer of a site, but it is possible that there would be other exemptions applicable depending on the value.
So if it were shortly there would be no question of a gift from you to your sister. But if it is in years to come, then you are looking at a possible rise in value of the house and so on which would complicate things.