Mega Spoilers if you haven't read all the routes yet
1) Why is Chase haunted by that spirit and who is it??
Chase is haunted by the spirit of Samuel Ayers, the man who died after being hit by Mr Bronson's (Sydney's dad) van. After Sam's death, his spirit possessed Mr Bronson
Sometime later, when Sydney and his dad are on a hunt, they quarrel with each other, and when Sydney runs off and Mr Bronson goes after him, they both stumble upon an abandoned white van. Mr Bronson recognizes it as the van which he killed Sam with. He starts acting weird and eventually shoots himself with the shotgun. After that, Sam's spirit, which had been in Bronson all the time, leaves his body and possesses Sydney.
Then, on the day when the main cast is at the Lake Emma, Sydney is playfully fighting with TJ (as always, since TJ is weak and Sydney loves wrestling), but then, seemingly because of Sam's possession, the situation escalates as the playful fight turns into an attempt to drown TJ in the lake. And this leads to ⬇️
2) What exactly happened to Sydney??
Sydney was drowned by Chase in Lake Emma after Sydney tried to drown TJ. Chase manages to intervene just in time to save TJ, and he starts fighting with Sydney. Driven by hate towards Sydney (both because of him always bullying/messing with TJ and because of the ongoing rumors that he's the one who killed Mr Bronson), Chase tries to drown Sydney. Whether Sydney is killed on the spot or later, when he is transported to the hospital - I don't remember. Either way, in that moment Sam's spirit leaves Sydney's body and possesses Chase.
When people asked them about Sydney's death, Chase fabricated a story claiming Sydney drowned while swimming in the lake to conceal his crime.
3) Why is Flynn such a mean bitch??
Sydney and Flynn were best friends, so as his other friends moved on, Flynn was deeply affected by his death. While everyone else had believed Chase's account of Sydney's death, Flynn knew that something was amiss. As TJ was the only witness of Sydney's demise, Flynn started pestering TJ with questions about the incident. TJ was always answering the same thing - that Sydney just drowned in the lake while swimming, but Flynn knew that was not true. The friend group started shielding TJ from Flynn, portraying Flynn as a bully and TJ as a victim, when in reality it was not like that at all
All in all, Flynn's 'bitching' stems from his wish to uncover the truth surrounding his best friend's fate, albeit in a less than amicable manner