Ok, I'm unsure if thread #4 is coming back --of course it had my best alt theory in it -- so I'm gonna try again and make some slight changes.
Two things are hard to overcome for me with the facts as I understand them, (that actually makes them not facts but opinions so they CANNOT be wrong).
* First: Why leave car up Pitcher Canyon? As stated before and for numerous reasons NOT a good location for a suspect to dump a car.
* Second: Why does no one seem to know where she was headed after class? It seems MC was keeping that secret herself, if so why?
My theory solves both of these. Here we go:
She sets up a meeting with (insert your prime suspect here). She has had or is having a relationship or possible some type of illegal dealings with this person. (I'm leaning towards relationship with older male.) Could be someone we've all been talking about, could be someone she has met through Gold's Gym. Older male makes it a double no-no and so she doesn't tell a soul this secret.
So, they make contact through cell phone and set up a place to meet, (it appears police are getting his cell phone records right now). They drive out towards Pitcher Canyon each in their own car until reaching end of pavement where she hops in with him. They go this way either because they have a destination they have gone to before, (empty house on market), or simply to take a drive up to snow-line, (maybe she has something to tell him???). Whatever it is she says, he doesn't take it well and in heat-of-moment strikes her using something probably not thought of as a weapon he has grabbed from his vehicle, (pickup?). The blow kills her. This is location 1.
It hits him what he has done. He runs through his mind for ideas. He's watched the Dexter series on cable tv. He wants to attempt something of that nature but he feels like a cornered animal up this dead-end canyon so he gets her body in the vehicle and drives out, passing MC's car along the way. From here he takes her to location 2. A place very familiar to him. He gets to work on what he thinks he can accomplish. (Watch any episode of Dexter and I think that is what he tried). He can't do it. He gives up, but figures he can still accomplish most of the plan. He just needs to get the body to a location where it won't be found and which he can pick up later by boat. He takes body out to CB, (location 3), leaving body very close to beach, but not so close as to be easily spotted. He breaks down here as well, not believing what he has done. He drives away with part of him actually hoping to get caught so he would never have to see that body and what he has done again. It really won't matter, he vividly pictures it all the time anyway.
There it is. Actually fairly simple, I think. Although there are some issues.
First: I know there is indications that the footprints left near her car were not hers. Personally, I think that scene was compromised, so no good footprints could have been found. Wasn't it just about dark when first officers arrived? Didn't the reporting party say he had got close enough to look in the backseat to see change of clothes? Maybe someone else had also checked it out?
Second: There is her cell phone usage. I think this is where LE is probably on the verge of out-right lying to us. We know they won't tell us who the last call was to, (very likely the prime-suspect), but just calling her isn't enough to focus on him or name him as a suspect. They need real evidence. He has gotten rid of the plastic sheeting and tools he used. Unless he slipped up somewhere with the evidence police will almost have to have his confession. My opinion is, they aren't gonna get it. By now, he's had time to justify what he's done and realized he can live with it. Police will likely have caught him in a half a dozen lies about his alibi but that doesn't actually prove anything either. Although suspects, (even innocent ones*), have been convicted with less. *Google "innocence project"
Now onward with the discussion.