Andy's and Karen's names were cleared during the events of Seed of Chucky.Why else would they do a Movie Within Movie about Chucky being the killer without any mention of Andy?
Tiffany tipped off Andy.She was still pissed at him for the events during Seed of Chucky so she played his game until he was delivered to Andy.
Nica died after she had her heart attack.The rest of the movie is her in Hell. Think about it, after she has her heart attack, she's almost never mobile. First, Ian has her hands strapped down so she can't move the chair on her own, and then Chucky throws her to the first floor through the banister, which caused her wheelchair to break. Then later, at the end of the film, Nica is found mentally unfit and is condemned to live in an asylum for the rest of her life. Seems like hell, right? Also, as Nica faints from her heart attack, we see Chucky approaching Ian from behind. Yet, we later see that Ian moved Nica from the garage and didn't even notice Chucky. Why would he approach him from behind if he wasn't going to do anything?
The Tommy Doll was actually John the Voodoo man.He wanted to keep a close eye on Andy and was willing to go against his religion to do it. He was not able to fully transfer his soul into that one, but enough so he could move around instead of speaking verbally to warn Andy. Hence why he was standing at the end of the stairs like he was waiting for Chucky.