This post will explain how Toby figured things out and went to find Dr. Sullivan

Many people ask and the answers were in front of you so I will bring examples from the episodes. Marlene also clarify a few things by tweeting about them, One of them was that everyone around the liars knew about Dr. Sullivan - for example ep 211 in the truck spoby talks about her. In Episode 212 Spencer says In fact that she have secrets and he deserves to be with someone else (let’s not forget ep 119 the “A” bag with ice at the motel). In Episode 215 she informs him “it just still not safe”. At 217 in conversation with Emily, he says - “I don’t think this is about me and her… i think it’s something else”.  later in the hospital Jenna informs him that Spencer is haunted. After he was injured (and Jenna said he wasn’t supposed go back to that house) Spencer broke up with him But not face to face ” why r u telling me this” means that she’s hiding something (because he knows her). Now you don’t have to be a brainiac to understand that the disappearance of Dr. Sullivan and someone is setting up the girls with a shovel is coincident (to be honest i’m surprised Toby was the only one that thought about that). At this point (after Jenna informed him that Spencer is haunted) he wants answers, and who is the best source - her therapist, which strangely disappeared, while everything had deteriorated. It is unclear if Anne told him about the identity of “A” (most likely not because he had scenes with Mona), but he knows someone is trying to hurt Spencer and it is no coincidence that she tried to break up with him (twice), although it was clear that she loves him and broke up with him for the wrong reasons. So in Episode 223 Toby trying to keep a distance (to keep Spencer safe - the woman he love) and in the process he try to get close to Jenna and gain back her trust - coase after the talk in the hospital it’s clear that she know something. 

Hope this post clarified some things for you :)