Don't remember if you mentioned them somewhere else, but I'd be interested to know what happened to the Lecarde sisters and to Vincent after PoR (and which ending is canon in your own canon).
OK so, the ending I consider canon for PoR would be the one where Jonathan uses the Vampire Killer to kill Dracula, and Vincent is cured.
After PoR, the first thing done was seal again the power of the Vampire Killer. This was a job done by the sisters.
Little time after that, Jonathan started displaying health issues. By studying the cause it was determined that Jonathan was still infected with a memory of Richter, and that this was causing his health to slowly decline. He used the whip MUCH less than his father, so he was not going to die, but his health was doomed to decline until he ended up forced to cease fighting, and he wasn't up to take that.
So, Charlotte and the sisters started studying a way to cure Jonathan, and even though they couldn't figure out a way to erase the memory, they eventually opted for another method. The sisters isolated the Richter memory on Jonathan's right hand, and took it off. Following this, Charlotte marked Jonathan with a glyph forged from his decepated hand -- Dextro Fio --, thus giving Jonathan the ability to materialize a new right hand from his arm through the power of the glyph (just like Shanoa could materialize wings using Volaticus).
Finally, in 1964, Stella had a child, and that is Cecilia Lang, which went to live with Jonathan by 1990. She inherited a weapon from him after being trained by her mother, which she uses to guard Jonathan's property.
Vincent simply returned to his tasks at the church, being mainly one of Charlotte's assistants as she rose amongst the ranks to become the most powerful sorcerer.
"Why Jonathan's right hand?"
Because Jonathan still planned to fight Dracula if no Belmont came. He's left handed, and his real left hand would need to be in contact with the whip for its power to work properly in 1999, if needed.