It seems I didn't give the Twilight Zone angle a fair shake. The books I was trying to find are:
1. Shades of Night, Falling (Sometimes called Harvest Moon) by <PERSON> (Published 2003)
2. A Gathering of Shadows by <PERSON> (Published 2003)
3. Deep in the Dark by <PERSON> (Published 2004)
They are part of a Twilight Zone trilogy. There seems to be very little information about them online which might be why I had a such a hard time finding them. Since asking the question, I have found and read all three books.
The trilogy follows two families: the <PERSON> and the <PERSON> in a small town, Geistadt, outside Brooklyn.
Book one is set in 1842 (So not medieval as I had thought). <PERSON> has traveled the world to learn the secrets of using magic. He wants thirteen sons for some magical reason. Twins <PERSON> and <PERSON> are his thirteenth and fourteenth sons, respectively by birth. <PERSON> gives <PERSON> everything he wants and trains him in using magic and essentially ignores <PERSON>. 1842 is the year of the twins' 21st birthday. The matriarch of the <PERSON> family at this time is <PERSON>. The <PERSON> and the <PERSON> have been feuding since <PERSON> moved to Geistadt.
Murders begin occurring once per day in Geistadt and the town attempts to discover the culprit.
Book two is set in 2002. <PERSON>' great-grandson <PERSON>, the thirteenth son of his father (who is also a thirteenth son) is working on a way to download human consciousness from the body. He calls this invention MindNet. 247
<PERSON>' spirit visits <PERSON> in dream-like encounters. <PERSON> eventually realizes that <PERSON> wants to use MindNet to retake a human form.
<PERSON> is the thirteenth daughter of <PERSON>'s great-great-grandson. She is doing a project for her graduate degree in Literature. Her project revolves around the ghost stories of <PERSON>. To help in her research, her father shows her the historical records kept by the <PERSON> family. As <PERSON> reads the records, she begins to interact with the spirit of <PERSON>. <PERSON>'s father also encourages her to meet-and hopefully marry-<PERSON>.
Book three is set in 2159. <PERSON> has perfected MindNet and human cloning meaning that he can move to a new, healthy body when needed. Essentially he has allowed those that can afford it to be immortal. His next goal is to revive <PERSON> from some of his blood that was preserved in a conopic jar while <PERSON> was alive. While attempting the resurrection, reality seems to unravel. Strange things start happening like buildings disappearing, adults reverting to infancy and trees appearing on the side of skyscrapers.
<PERSON> (called <PERSON> in the question) is a police cadet at the time and a <PERSON> descendant. She has a phone implanted in her jaw. <PERSON>'s spirit (called <PERSON> in the question) reaches out to her and asks for her help in stopping the craziness. She finds where his spirit is trapped and he enters her body where she can talk to him. He directs her to a <PERSON> descendant, <PERSON>, and together they head to the building where <PERSON> is attempting to revive <PERSON>. 715