I am in the graveyard and Jack is noware in sight. I am at the end in the sequence where I am supposed to put the tombstone on the graves but Jack isn't there.

First off, it says in the walkthrough to sort out who's who on the eight gravestones and then it says to dig your own grave. Also:
.
.
.
.
.
.
.
.
.
.
.
.
.
.
"Exit Alicia's room, and go listen at Jack's doorway. He is drunk and hallucinating about Mary Rose. Go to Mary Rose's room, take the dress from her closet and put it on. Cuuuute! Really goes with that goatee! Go visit Jack, frightening him. Mynah, Mother's Little Helper, is sitting right there on the newel-post. He becomes your Mary-Rose voice. At the end of the conversation with Jack, you will have the Library key."

Have you tried any of that??????

Deecar, the same thing happened to me. I had a terrible time with this game technically, with many crashes, freezes, missing cursors, etc. When I got to the graveyard Jack wasn't there either. I checked several wt's to make sure I did everything. And I did but still no Jack. At first I didn't go to the shed but then I did and still no Jack. All the wt's said that he would confront me, but he never did even when I finally got him to appear. What I eventually did was shut down the game and then go back to my last save. With this game I made a habit of saving every 5 minutes or so especially when I entered a new scene or knew a closeup was coming (my game would usually freeze, crash or I'd have no control over the cursor for about 5 minutes while the closeup was trying to spin up). By shutting down the game and reloading my save - I was still in the graveyard at this point and suddenly Jack appeared and I was able to complete the grave sequence (and finally the game!!). Try that. I hope this works for you. And note: I never was able to get a confrontation from him, but I did get him to show up and have him follow me as I placed the gravestones.

Good luck!!