meow

Go for it.  I am applying to engineering programs, so obviously the requirements will be very different.

What is your thesis advisor's position now? Is he still a postdoc elsewhere, or is he now a tenure-track professor?
-- If Person 0 (thesis advisor) is now a tenure-tracked professor, then I think you should get the following three letters as your main LORs, in order of how important they would be:
0. Thesis Advisor
2. Assistant Professor with one class
1. Industry Manager
You might also want to consider submitting Prof #4 (full prof) as a 4th LOR so that you have a senior professor there and it sounds like he will be able to write a decent letter.
-- If Person 0  (thesis advisor) is still a postdoc or in academia but in a term position rather than a permanent position, then I would definitely submit all 4 letters. In places where I could not submit 4 letters, I would replace Prof #2 with Prof #4.
-- If Person 0 is not in academia anymore, I would submit all 4 letters if possible. If not possible, this would be tough because you would really want two letters to be from academia, which means Prof 2 and Prof 4 and now you have to decide between Thesis Advisor or industry manager. I would probably pick thesis advisor in this case as industry manager does not have a PhD.
Finally, it sounds like you are concerned Prof #2 asked you to feed her a lot of information. I don't think this is a problem at all and it is actually quite normal for a LOR. The information you provide her will allow her to generate examples in her letter!
 

loveor, is your thesis advisor in the UK/Australia? Because, if so, then lecturers are often the equivalent of an "assistant professor" in the US system. If that's the case, then it is entirely appropriate to get a recommendation letter from someone with that status, especially if they have a PhD.

I agree that if Professor #2 is still in academia (just not at your original university), then she is clearly the best choice to ask for the 2nd letter. 
I think that if you can secure Professor #2's letter then I think the best choice for letter #3 is your industry job's manager. I am assuming your industry job is at least vaguely connected to the field you did your undergrad in and what you're apply to for grad school. (I make this assumption because in my field, when we say "industry", we mean a non-academic job related to our research, not just any non-academic job!) I agree with fuzzy that It's not ideal that they are not academia, but in my opinion, the "all letters must be academic" advice really only applies to applicants straight out of undergrad. Since you have graduated and spent a couple of years working in a related field, it makes sense to get a letter from your job that attests to your expertise.
So, if both the above suggestions work out, you should have all three letters. At this point, I think it's up to you if you want to add a fourth letter (with either Prof #3 or Prof #4) as fuzzy suggests. It would be nice to have a 3rd academic LOR just in case. But sometimes, having weaker LORs along with strong ones can "dilute" them. This is hard to gauge.
On the other hand, if your industry job is not connected to your undergrad degree nor your future graduate program then I am less sure about a letter from your manager being letter #3 (maybe it can be letter #4 though). In this case, if you can still get a letter from Prof #2, then I think letter #3 should come from Prof #3 or Prof #4. You can certainly send them copies of your old submitted work to remind them of the quality of work you did in their class. In addition, if they provided feedback on your final essays and projects, you might even send them a corrected version that implements their suggestions.

I assume, though you didn't say, that this would be for a research-based PhD program. My answer will likely be different under different circumstances. For a PhD, you should have at least two academic references. Generally it's better if all three are from academics, but if we're comparing a weak "did well in class" letter to a glowing one from industry, it seems to me that the strong letter is a better choice. (Another option to look into whether the schools you're applying to might allow you to submit additional letters beyond the required minimum, in which case you could submit 3 academic + 1 from industry, and cover all your bases.)
Thoughts on your academic options:
- Professor #2 seems like the best option here, from what I can tell. She's seen you both in class and outside it, and has recommended that you do a PhD before, so she clearly thinks you're capable. The fact that she's no longer affiliated with your university is not an issue, IF that just means that she took another job in the meanwhile. If she left academia, that's a different story altogether. 
- Professor #3 might have seen you more in class, but it doesn't sound like there is much for him to go off of beyond that. I wonder if there are ways to help him get to know you and your research ideas better. Maybe through a conversation or through having him read your SOP and/or any papers you have that you're proud of. As it stands, this will probably be my second choice after #2. 
- Professor #4 again sounds like someone who wouldn't really know you well. You say you hope he kept a copy of your report; that may depend on the submission system. Do you have a copy of this report? Again, this would be a decent option just in case you can provide him with additional information that he could use to write you a letter that goes beyond just "myhaeon was in my class and got an A." 
Do these professors know each other? One option you might consider is asking Prof #2 to chat with you about grad school applications over the phone/Skype. Unless she's no longer in academia, you should ask her for a letter. When you talk, you can also consult with her about whether a letter from Prof #3/4 is a good idea compared to a letter from your boss. Another factor in deciding between these professors that you didn't mention is how well-known they are. If you're going to get a not-that-awesome letter, it'd be better if it came from someone famous than from someone unknown. 
 
ETA: although you didn't ask, being out of school for two years and doing something else is not going to hurt your chances and isn't something you should regret. You have valuable experience that will come in handy as a student. People who go straight from school to college to grad school sometimes miss on vital experiences of the "real world," so to speak. Academia is a whole different kind of world in many ways, and it's worth actually knowing what's out there and that you do want to be in academia, not because that's just the natural progression of things, but because you tried it and you know what work for you and what doesn't.