Question: What happened to Doc's girlfriend from the first film? She risked her life to be with him at the end of Young Guns, so its a little odd that there's no mention of her in this film.
Answer: During the ending monologue from the first film, it is revealed that Doc moved east with a "celestial bride, her mother and 14 brothers and sisters."
Question: What was in the red backpack that John Ritter was going to give Michael Richards as ransom for Jr, since he didn't have the 100 grand that he promised him?
Question: Why did Jack and Max try to kill Mason's son Sonny? They have their masks on and there's no way that Sonny would have identified them.
Answer: The cover story was that it was a drug deal gone wrong, which led to the murders. The child witnessed them planting evidence and would be able to blow the cover story.
Answer: He survived the first attempt of his family's murder. There's no telling what he saw or heard. As for the masks, the bad guys were taking no chances, security cameras, cell phones and the unexpected eyewitness.
Cell phones? I don't recall seeing a cell phone in the entire movie. It was all landline phones. Cell phones didn't really start to get used until around the mid-90s (a few years later).
Question: When Peyton wakes up in the hospital, images suddenly appear. What exactly is the significance of the light bulb shattering and the little marionette with the huge head supposed to represent?
Answer: It's just psychedelic imagery to try and show his fragile state of mind and how he's losing it. The shattering light-bulb is likely to show that his mind is "shattering" (as light-bulbs appearing above someone's head are often used to signify brains/ideas in fictional, particularly cartoons), and the marionette "dancing" is the first part of the recurring motif in which he sees himself as a "freak." (Which is paid off later when he starts singing a demented song about "Paying five bucks to see the dancing freak!").
Answer: Doc says in the movie he is married with kids. So you have to assume he married her.