Aoya sure spent an entire chapter setting up foreshadowing huh. Though I'd be surprised if he turns out to have actually been behind all of this from the very start considering he got roped into taking part by the detective. Also who the fuck takes their little sister to their murders come on man.
Well he was extremely sus from how he pressured Tokiko to come to the house alone, but him mentioning the kitchen pretty much cleared any doubt that he was up to no good. Tokiko mentioning that they "don't" know the layout and him mentioning the door were almost a bit too much.
Thing is, though, that many of the deaths around Tokiko were too clearly accidental for him to plan, so I don't think he's as much a mastermind as he thinks he is, and Tokiko is much harder to kill than he's accounting for. I mean she managed to survive her uncle stabbing her repeatedly, with him ending up dead instead... there's more to this story than just a flesh and bones killer.
I think there are indeed three interwoven elements to this. Aoya killed the Shirokis and Tokiko's teacher two years ago as well as Rina but he probably isn't responsible for the other 22 bodies. The other deaths of the Kurosu family, maybe going all the way back to Tokiko's biological parents (fate unknown), might be a case that's more attractive to Akiyama and the professor. The 22 bodies might be related to Tokiko's biological parents, who knows.