BabyScientist

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

It sounds like you'd be a solid applicant for PhD programs and would have a unique perspective.
I've enjoyed my experience thus far. I love research, and it's what I get to do.
Best aspect: Freedom. I guess this depends on your mentor but mine is very open to my ideas and I, with guidance, mostly make my own decisions. My day is dictated by what I want.
Worst aspect: Frankly, you'd make a lot more as a PT. The PhD stipend is, on average, around $30k a year. So you're making around that much for 5-6 years, then if you do a postdoc you make maybe $40-50k a year for the 3-5 years of that. Unless you want to go into industry, then you could make a lot more after your PhD.
That being said, I love what I do and am not doing it for the money. If you truly hate what you're doing, and enjoy the research you're doing, it sounds like a great idea to apply for PhD programs. And I admire your commitment to finish what you've started. Good luck!

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

The trick is to have an appropriate range of schools. I applied to 10 and it ended up being too many. Unless you have the money to spend, don't bother. Just make sure every school you apply to has at least 3 faculty you'd be excited to work with. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

I'm still waiting for Harvard to reject me. 
I'm a second year PhD student. 

Brown

There's still a chance, but now is the time to consider backup plans.
Take a look at your application and decide what needs improvement. A masters isn't necessarily the next step. Assuming you're applying from undergrad, maybe what you need is a full time lab position

You're over thinking it. You don't have to ask questions about their research. If questions didn't just come to me, I tried to relate their work to mine, or to things I'd heard of. If pipe in with like "oh I read something about that technique" or "oh my lab was exploring that".
More important than asking questions about their research is asking questions about the program and the logistics of their lab. 
If you actually want to work with them, absolutely ask if they're taking students.
Other good questions to ask:
How big is your lab? Where is your funding from? Do you think the coursework in this program is valuable. Do students in your lab go to conferences? What do your students go on to do after graduating? 

Most interviews go like this:
They ask you about your research experience. You start telling them about it, they occasionally stop you to ask questions.
They tell you about their research (this is why reading papers in advance is unnecessary). Ideally, you try to ask questions or relate their work to yours or things you've heard of.
They ask you if you have any questions about the program. You ask questions about how their lab works (how big it is, if they send people to conferences, if they have space for you, where their funding comes from, what their students go on to do, etc). This shows them you know what goes into a PhD.
You shouldn't be focused on one particular line of research. You should be open to studying many things within the general field. If that's the only professor studying it at that school but he isn't taking students, they won't accept you. Or if multiple do but aren't taking students, same thing.
You should show that you're excited to talk about your own work, you are able to think about other people's work (by asking questions about their research), you know what goes into a PhD, and you know why you want a PhD. If you're not sure about the why, they'll likely be able to tell, and they won't want to accept anyone who might end up quitting their PhD.

There isn't really any point. Request them for interviews when they're making your schedule, and you'll be able to talk to them in person. The interview is more of a meeting than an interview. It's a chance for you to get to know them and ask all your questions as much as it's a chance for them to see your personality.

Most interviews go like this:
They ask you about your research experience. You start telling them about it, they occasionally stop you to ask questions.
They tell you about their research (this is why reading papers in advance is unnecessary). Ideally, you try to ask questions or relate their work to yours or things you've heard of.
They ask you if you have any questions about the program. You ask questions about how their lab works (how big it is, if they send people to conferences, if they have space for you, where their funding comes from, what their students go on to do, etc). This shows them you know what goes into a PhD.
You shouldn't be focused on one particular line of research. You should be open to studying many things within the general field. If that's the only professor studying it at that school but he isn't taking students, they won't accept you. Or if multiple do but aren't taking students, same thing.
You should show that you're excited to talk about your own work, you are able to think about other people's work (by asking questions about their research), you know what goes into a PhD, and you know why you want a PhD. If you're not sure about the why, they'll likely be able to tell, and they won't want to accept anyone who might end up quitting their PhD.